diff --git a/.gitignore b/.gitignore index 4feeb36c3..66fe55aa9 100644 --- a/.gitignore +++ b/.gitignore @@ -20,5 +20,5 @@ /*/build /build spark-warehouse -/*/*/job-override.properties +/**/job-override.properties diff --git a/dhp-build/dhp-build-assembly-resources/pom.xml b/dhp-build/dhp-build-assembly-resources/pom.xml index 834af77fa..0c4637def 100644 --- a/dhp-build/dhp-build-assembly-resources/pom.xml +++ b/dhp-build/dhp-build-assembly-resources/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build-assembly-resources diff --git a/dhp-build/dhp-build-properties-maven-plugin/pom.xml b/dhp-build/dhp-build-properties-maven-plugin/pom.xml index 4f99d5298..308d78715 100644 --- a/dhp-build/dhp-build-properties-maven-plugin/pom.xml +++ b/dhp-build/dhp-build-properties-maven-plugin/pom.xml @@ -6,7 +6,7 @@ eu.dnetlib.dhp dhp-build - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build-properties-maven-plugin @@ -76,6 +76,41 @@ + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + + org.apache.maven.plugins + + + maven-plugin-plugin + + + [3.2,) + + + descriptor + + + + + + + + + + + + diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index e0b20204c..e471af76d 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-build pom diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 43c2a3834..4416bd4ff 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT ../ @@ -42,6 +42,10 @@ com.rabbitmq amqp-client + + net.sf.saxon + Saxon-HE + diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java new file mode 100644 index 000000000..bd3962440 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java @@ -0,0 +1,32 @@ +package eu.dnetlib.dhp.utils.saxon; + +import net.sf.saxon.expr.XPathContext; +import net.sf.saxon.lib.ExtensionFunctionCall; +import net.sf.saxon.lib.ExtensionFunctionDefinition; +import net.sf.saxon.om.Sequence; +import net.sf.saxon.om.StructuredQName; +import net.sf.saxon.trans.XPathException; + +public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition { + + public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension"; + + public abstract String getName(); + public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException; + + @Override + public StructuredQName getFunctionQName() { + return new StructuredQName("dnet", DEFAULT_SAXON_EXT_NS_URI, getName()); + } + + @Override + public ExtensionFunctionCall makeCallExpression() { + return new ExtensionFunctionCall() { + @Override + public Sequence call(XPathContext context, Sequence[] arguments) throws XPathException { + return doCall(context, arguments); + } + }; + } + +} \ No newline at end of file diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java new file mode 100644 index 000000000..f90e2a23e --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java @@ -0,0 +1,67 @@ +package eu.dnetlib.dhp.utils.saxon; + +import net.sf.saxon.expr.XPathContext; +import net.sf.saxon.om.Item; +import net.sf.saxon.om.Sequence; +import net.sf.saxon.trans.XPathException; +import net.sf.saxon.value.SequenceType; +import net.sf.saxon.value.StringValue; + +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Calendar; +import java.util.GregorianCalendar; + +public class ExtractYear extends AbstractExtensionFunction { + + private static final String[] dateFormats = { "yyyy-MM-dd", "yyyy/MM/dd" }; + + @Override + public String getName() { + return "extractYear"; + } + + @Override + public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException { + if (arguments == null | arguments.length == 0) { + return new StringValue(""); + } + final Item item = arguments[0].head(); + if (item == null) { + return new StringValue(""); + } + return new StringValue(_year(item.getStringValue())); + } + + @Override + public int getMinimumNumberOfArguments() { + return 0; + } + + @Override + public int getMaximumNumberOfArguments() { + return 1; + } + + @Override + public SequenceType[] getArgumentTypes() { + return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + } + + @Override + public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) { + return SequenceType.SINGLE_STRING; + } + + private String _year(String s) { + Calendar c = new GregorianCalendar(); + for (String format : dateFormats) { + try { + c.setTime(new SimpleDateFormat(format).parse(s)); + String year = String.valueOf(c.get(Calendar.YEAR)); + return year; + } catch (ParseException e) {} + } + return ""; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java new file mode 100644 index 000000000..634e08788 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java @@ -0,0 +1,66 @@ +package eu.dnetlib.dhp.utils.saxon; + +import net.sf.saxon.expr.XPathContext; +import net.sf.saxon.om.Sequence; +import net.sf.saxon.trans.XPathException; +import net.sf.saxon.value.SequenceType; +import net.sf.saxon.value.StringValue; + +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.Date; + +public class NormalizeDate extends AbstractExtensionFunction { + + private static final String[] normalizeDateFormats = { "yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy" }; + + private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'"); + + @Override + public String getName() { + return "normalizeDate"; + } + + @Override + public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException { + if (arguments == null | arguments.length == 0) { + return new StringValue(""); + } + String s = arguments[0].head().getStringValue(); + return new StringValue(_year(s)); + } + + @Override + public int getMinimumNumberOfArguments() { + return 0; + } + + @Override + public int getMaximumNumberOfArguments() { + return 1; + } + + @Override + public SequenceType[] getArgumentTypes() { + return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + } + + @Override + public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) { + return SequenceType.SINGLE_STRING; + } + + private String _year(String s) { + final String date = s != null ? s.trim() : ""; + + for (String format : normalizeDateFormats) { + try { + Date parse = new SimpleDateFormat(format).parse(date); + String res = new SimpleDateFormat(normalizeOutFormat).format(parse); + return res; + } catch (ParseException e) {} + } + return ""; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java new file mode 100644 index 000000000..a221e37c6 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java @@ -0,0 +1,60 @@ +package eu.dnetlib.dhp.utils.saxon; + +import net.sf.saxon.expr.XPathContext; +import net.sf.saxon.om.Item; +import net.sf.saxon.om.Sequence; +import net.sf.saxon.trans.XPathException; +import net.sf.saxon.value.SequenceType; +import net.sf.saxon.value.StringValue; +import org.apache.commons.lang3.StringUtils; + +public class PickFirst extends AbstractExtensionFunction { + + @Override + public String getName() { + return "pickFirst"; + } + + @Override + public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException { + if (arguments == null | arguments.length == 0) { + return new StringValue(""); + } + + final String s1 = getValue(arguments[0]); + final String s2 = getValue(arguments[1]); + + return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : ""); + } + + private String getValue(final Sequence arg) throws XPathException { + if (arg != null) { + final Item item = arg.head(); + if (item != null) { + return item.getStringValue(); + } + } + return ""; + } + + @Override + public int getMinimumNumberOfArguments() { + return 0; + } + + @Override + public int getMaximumNumberOfArguments() { + return 2; + } + + @Override + public SequenceType[] getArgumentTypes() { + return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; + } + + @Override + public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) { + return SequenceType.SINGLE_STRING; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java new file mode 100644 index 000000000..611709ff0 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java @@ -0,0 +1,30 @@ +package eu.dnetlib.dhp.utils.saxon; + +import net.sf.saxon.Configuration; +import net.sf.saxon.TransformerFactoryImpl; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.stream.StreamSource; +import java.io.StringReader; + +public class SaxonTransformerFactory { + + /** + * Creates the index record transformer from the given XSLT + * @param xslt + * @return + * @throws TransformerException + */ + public static Transformer newInstance(final String xslt) throws TransformerException { + + final TransformerFactoryImpl factory = new TransformerFactoryImpl(); + final Configuration conf = factory.getConfiguration(); + conf.registerExtensionFunction(new ExtractYear()); + conf.registerExtensionFunction(new NormalizeDate()); + conf.registerExtensionFunction(new PickFirst()); + + return factory.newTransformer(new StreamSource(new StringReader(xslt))); + } + +} diff --git a/dhp-schemas/README.md b/dhp-schemas/README.md index 473ad4cf1..7431cda42 100644 --- a/dhp-schemas/README.md +++ b/dhp-schemas/README.md @@ -1,3 +1,11 @@ Description of the project -------------------------- -This project defines **serialization schemas** of Avro data store files that are used to pass data between workflow nodes in the system. +This project defines **object schemas** of the OpenAIRE main entities and the relationships that intercur among them. +Namely it defines the model for + +- **research product (result)** which subclasses in publication, dataset, other research product, software +- **data source** object describing the data provider (institutional repository, aggregators, cris systems) +- **organization** research bodies managing a data source or participating to a research project +- **project** research project + +Te serialization of such objects (data store files) are used to pass data between workflow nodes in the processing pipeline. diff --git a/dhp-schemas/pom.xml b/dhp-schemas/pom.xml index 20896a61d..d8873d33d 100644 --- a/dhp-schemas/pom.xml +++ b/dhp-schemas/pom.xml @@ -5,7 +5,7 @@ eu.dnetlib.dhp dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT ../ @@ -26,6 +26,11 @@ commons-lang3 + + com.fasterxml.jackson.core + jackson-databind + + eu.dnetlib.dhp dhp-common diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java new file mode 100644 index 000000000..e81120e42 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java @@ -0,0 +1,15 @@ +package eu.dnetlib.dhp.schema.oaf; + +public class Country extends Qualifier { + + private DataInfo dataInfo; + + public DataInfo getDataInfo() { + return dataInfo; + } + + public void setDataInfo(DataInfo dataInfo) { + this.dataInfo = dataInfo; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java index f52a500fe..032468de2 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java @@ -40,9 +40,9 @@ public class Datasource extends OafEntity implements Serializable { private List> odlanguages; - private List< Field> odcontenttypes; + private List> odcontenttypes; - private List< Field> accessinfopackage; + private List> accessinfopackage; // re3data fields private Field releasestartdate; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java index 43af60286..1839fbd53 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; +import com.fasterxml.jackson.annotation.JsonIgnore; import org.apache.commons.lang3.StringUtils; import java.io.Serializable; @@ -36,7 +37,7 @@ public class GeoLocation implements Serializable { this.place = place; } - + @JsonIgnore public boolean isBlank() { return StringUtils.isBlank(point) && StringUtils.isBlank(box) && diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java index 8f852af65..f82296d8b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java @@ -22,6 +22,14 @@ public class Instance implements Serializable { private Field dateofacceptance; + // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results + private Field processingchargeamount; + + // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results + private Field processingchargecurrency; + + private Field refereed; //peer-review status + public Field getLicense() { return license; } @@ -86,7 +94,29 @@ public class Instance implements Serializable { this.dateofacceptance = dateofacceptance; } + public Field getProcessingchargeamount() { + return processingchargeamount; + } + public void setProcessingchargeamount(Field processingchargeamount) { + this.processingchargeamount = processingchargeamount; + } + + public Field getProcessingchargecurrency() { + return processingchargecurrency; + } + + public void setProcessingchargecurrency(Field processingchargecurrency) { + this.processingchargecurrency = processingchargecurrency; + } + + public Field getRefereed() { + return refereed; + } + + public void setRefereed(Field refereed) { + this.refereed = refereed; + } public String toComparableString(){ return String.format("%s::%s::%s::%s", diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java index 74d9f77bd..5a841b96f 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; +import com.fasterxml.jackson.annotation.JsonIgnore; import org.apache.commons.lang3.StringUtils; import java.io.Serializable; @@ -40,6 +41,7 @@ public class KeyValue implements Serializable { return isBlank()?"":String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : ""); } + @JsonIgnore public boolean isBlank() { return StringUtils.isBlank(key) && StringUtils.isBlank(value); } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java index 7e4660f4b..ae2bf1a60 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; +import com.fasterxml.jackson.annotation.JsonIgnore; import org.apache.commons.lang3.StringUtils; import java.io.Serializable; @@ -50,6 +51,8 @@ public class Qualifier implements Serializable { schemeid != null ? schemeid : "", schemename != null ? schemename : ""); } + + @JsonIgnore public boolean isBlank() { return StringUtils.isBlank(classid) && StringUtils.isBlank(classname) && diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index eb5572ce1..5cb04da5e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -1,10 +1,8 @@ package eu.dnetlib.dhp.schema.oaf; -import org.apache.commons.lang3.StringUtils; - import java.io.Serializable; -import java.util.*; -import java.util.stream.Collectors; +import java.util.Comparator; +import java.util.List; public abstract class Result extends OafEntity implements Serializable { @@ -16,7 +14,7 @@ public abstract class Result extends OafEntity implements Serializable { // common fields private Qualifier language; - private List country; + private List country; private List subject; @@ -44,16 +42,10 @@ public abstract class Result extends OafEntity implements Serializable { private List> coverage; - private Field refereed; //peer-review status + private Qualifier bestaccessright; private List context; - // ( article | book ) processing charges. Defined here to cope with possible wrongly typed results - private Field processingchargeamount; - - // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results - private Field processingchargecurrency; - private List externalReference; private List instance; @@ -82,11 +74,11 @@ public abstract class Result extends OafEntity implements Serializable { this.language = language; } - public List getCountry() { + public List getCountry() { return country; } - public void setCountry(List country) { + public void setCountry(List country) { this.country = country; } @@ -194,12 +186,12 @@ public abstract class Result extends OafEntity implements Serializable { this.coverage = coverage; } - public Field getRefereed() { - return refereed; + public Qualifier getBestaccessright() { + return bestaccessright; } - public void setRefereed(Field refereed) { - this.refereed = refereed; + public void setBestaccessright(Qualifier bestaccessright) { + this.bestaccessright = bestaccessright; } public List getContext() { @@ -226,24 +218,6 @@ public abstract class Result extends OafEntity implements Serializable { this.instance = instance; } - public Field getProcessingchargeamount() { - return processingchargeamount; - } - - public Result setProcessingchargeamount(Field processingchargeamount) { - this.processingchargeamount = processingchargeamount; - return this; - } - - public Field getProcessingchargecurrency() { - return processingchargecurrency; - } - - public Result setProcessingchargecurrency(Field processingchargecurrency) { - this.processingchargecurrency = processingchargecurrency; - return this; - } - @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); @@ -287,19 +261,9 @@ public abstract class Result extends OafEntity implements Serializable { coverage = mergeLists(coverage, r.getCoverage()); - if (r.getRefereed() != null && compareTrust(this, r) < 0) - refereed = r.getRefereed(); - context = mergeLists(context, r.getContext()); - if (r.getProcessingchargeamount() != null && compareTrust(this, r) < 0) - processingchargeamount = r.getProcessingchargeamount(); - - if (r.getProcessingchargecurrency() != null && compareTrust(this, r) < 0) - processingchargecurrency = r.getProcessingchargecurrency(); - externalReference = mergeLists(externalReference, r.getExternalReference()); - } @@ -314,5 +278,4 @@ public abstract class Result extends OafEntity implements Serializable { return a.size() > b.size() ? a : b; } - } diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 328e783c4..78831073f 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -4,7 +4,7 @@ eu.dnetlib.dhp dhp-workflows - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT dhp-aggregation @@ -25,6 +25,12 @@ dhp-common ${project.version} + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + net.sf.saxon @@ -44,6 +50,17 @@ jaxen jaxen + + + org.mongodb + mongo-java-driver + + + + org.postgresql + postgresql + 42.2.10 + org.mockito diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java new file mode 100644 index 000000000..e91a53045 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java @@ -0,0 +1,236 @@ +package eu.dnetlib.dhp.migration; + +import java.io.Closeable; +import java.io.IOException; +import java.net.URI; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.codehaus.jackson.map.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.ExtraInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OAIProvenance; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OriginDescription; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class AbstractMigrationExecutor implements Closeable { + + private final AtomicInteger counter = new AtomicInteger(0); + + private final Text key = new Text(); + + private final Text value = new Text(); + + private final ObjectMapper objectMapper = new ObjectMapper(); + + private final SequenceFile.Writer writer; + + private static final Log log = LogFactory.getLog(AbstractMigrationExecutor.class); + + public AbstractMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception { + + log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser)); + + this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer + .keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class)); + } + + private Configuration getConf(final String hdfsNameNode, final String hdfsUser) throws IOException { + final Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + System.setProperty("HADOOP_USER_NAME", hdfsUser); + System.setProperty("hadoop.home.dir", "/"); + FileSystem.get(URI.create(hdfsNameNode), conf); + return conf; + } + + protected void emitOaf(final Oaf oaf) { + try { + key.set(counter.getAndIncrement() + ":" + oaf.getClass().getSimpleName().toLowerCase()); + value.set(objectMapper.writeValueAsString(oaf)); + writer.append(key, value); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + writer.hflush(); + writer.close(); + } + + public static KeyValue keyValue(final String k, final String v) { + final KeyValue kv = new KeyValue(); + kv.setKey(k); + kv.setValue(v); + return kv; + } + + public static List listKeyValues(final String... s) { + if (s.length % 2 > 0) { throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)"); } + + final List list = new ArrayList<>(); + for (int i = 0; i < s.length; i += 2) { + list.add(keyValue(s[i], s[i + 1])); + } + return list; + } + + public static Field field(final T value, final DataInfo info) { + if (value == null || StringUtils.isBlank(value.toString())) { return null; } + + final Field field = new Field<>(); + field.setValue(value); + field.setDataInfo(info); + return field; + } + + public static List> listFields(final DataInfo info, final String... values) { + return Arrays.stream(values).map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList()); + } + + public static List> listFields(final DataInfo info, final List values) { + return values.stream().map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList()); + } + + public static Qualifier qualifier(final String classid, final String classname, final String schemeid, final String schemename) { + final Qualifier q = new Qualifier(); + q.setClassid(classid); + q.setClassname(classname); + q.setSchemeid(schemeid); + q.setSchemename(schemename); + return q; + } + + public static StructuredProperty structuredProperty(final String value, + final String classid, + final String classname, + final String schemeid, + final String schemename, + final DataInfo dataInfo) { + + return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo); + } + + public static StructuredProperty structuredProperty(final String value, final Qualifier qualifier, final DataInfo dataInfo) { + if (value == null) { return null; } + final StructuredProperty sp = new StructuredProperty(); + sp.setValue(value); + sp.setQualifier(qualifier); + sp.setDataInfo(dataInfo); + return sp; + } + + public static ExtraInfo extraInfo(final String name, final String value, final String typology, final String provenance, final String trust) { + final ExtraInfo info = new ExtraInfo(); + info.setName(name); + info.setValue(value); + info.setTypology(typology); + info.setProvenance(provenance); + info.setTrust(trust); + return info; + } + + public static OAIProvenance oaiIProvenance(final String identifier, + final String baseURL, + final String metadataNamespace, + final Boolean altered, + final String datestamp, + final String harvestDate) { + + final OriginDescription desc = new OriginDescription(); + desc.setIdentifier(identifier); + desc.setBaseURL(baseURL); + desc.setMetadataNamespace(metadataNamespace); + desc.setAltered(altered); + desc.setDatestamp(datestamp); + desc.setHarvestDate(harvestDate); + + final OAIProvenance p = new OAIProvenance(); + p.setOriginDescription(desc); + + return p; + } + + public static Journal journal(final String name, + final String issnPrinted, + final String issnOnline, + final String issnLinking, + final String ep, + final String iss, + final String sp, + final String vol, + final String edition, + final String conferenceplace, + final String conferencedate, + final DataInfo dataInfo) { + + if (StringUtils.isNotBlank(name) || StringUtils.isNotBlank(issnPrinted) || StringUtils.isNotBlank(issnOnline) || StringUtils.isNotBlank(issnLinking)) { + final Journal j = new Journal(); + j.setName(name); + j.setIssnPrinted(issnPrinted); + j.setIssnOnline(issnOnline); + j.setIssnLinking(issnLinking); + j.setEp(ep); + j.setIss(iss); + j.setSp(sp); + j.setVol(vol); + j.setEdition(edition); + j.setConferenceplace(conferenceplace); + j.setConferencedate(conferencedate); + j.setDataInfo(dataInfo); + return j; + } else { + return null; + } + } + + public static DataInfo dataInfo(final Boolean deletedbyinference, + final String inferenceprovenance, + final Boolean inferred, + final Boolean invisible, + final Qualifier provenanceaction, + final String trust) { + final DataInfo d = new DataInfo(); + d.setDeletedbyinference(deletedbyinference); + d.setInferenceprovenance(inferenceprovenance); + d.setInferred(inferred); + d.setInvisible(invisible); + d.setProvenanceaction(provenanceaction); + d.setTrust(trust); + return d; + } + + public static String createOpenaireId(final int prefix, final String originalId) { + final String nsPrefix = StringUtils.substringBefore(originalId, "::"); + final String rest = StringUtils.substringAfter(originalId, "::"); + return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest)); + + } + + public static String asString(final Object o) { + return o == null ? "" : o.toString(); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java new file mode 100644 index 000000000..00d1aa60d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java @@ -0,0 +1,439 @@ +package eu.dnetlib.dhp.migration; + +import java.io.IOException; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.DocumentFactory; +import org.dom4j.DocumentHelper; +import org.dom4j.Node; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.OAIProvenance; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor { + + protected final Map code2name = new HashMap<>(); + + protected final MdstoreClient mdstoreClient; + + protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title"); + + protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER = + qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies"); + protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies"); + + private static final Log log = LogFactory.getLog(AbstractMongoExecutor.class); + + public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, + final String mongoDb, final String dbUrl, final String dbUser, + final String dbPassword) throws Exception { + + super(hdfsPath, hdfsNameNode, hdfsUser); + + this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb); + loadClassNames(dbUrl, dbUser, dbPassword); + + final Map nsContext = new HashMap<>(); + + registerNamespaces(nsContext); + + DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); + } + + private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException { + + log.info("Loading vocabulary terms from db..."); + + try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) { + code2name.clear(); + dbClient.processResults("select code, name from class", rs -> { + try { + code2name.put(rs.getString("code"), rs.getString("name")); + } catch (final SQLException e) { + e.printStackTrace(); + } + }); + } + + log.info("Found " + code2name.size() + " terms."); + + } + + public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException { + + log.info(String.format("Searching mdstores (format: %s, layout: %s, interpretation: %s)", mdFormat, mdLayout, mdInterpretation)); + + final Map colls = mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation); + log.info("Found " + colls.size() + " mdstores"); + + for (final Entry entry : colls.entrySet()) { + log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")"); + final String currentColl = entry.getValue(); + + for (final String xml : mdstoreClient.listRecords(currentColl)) { + final Document doc = DocumentHelper.parseText(xml); + + final String type = doc.valueOf("//dr:CobjCategory/@type"); + final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name")); + final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom + : keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name")); + + final DataInfo info = prepareDataInfo(doc); + final long lastUpdateTimestamp = new Date().getTime(); + + for (final Oaf oaf : createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp)) { + emitOaf(oaf); + } + } + } + log.info("All Done."); + } + + protected void registerNamespaces(final Map nsContext) { + nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr"); + nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri"); + nsContext.put("oaf", "http://namespace.openaire.eu/oaf"); + nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/"); + nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance"); + } + + protected List createOafs(final Document doc, + final String type, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List oafs = new ArrayList<>(); + + switch (type.toLowerCase()) { + case "": + case "publication": + final Publication p = new Publication(); + populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER); + p.setJournal(prepareJournal(doc, info)); + oafs.add(p); + break; + case "dataset": + final Dataset d = new Dataset(); + populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + d.setResulttype(DATASET_RESULTTYPE_QUALIFIER); + d.setStoragedate(prepareDatasetStorageDate(doc, info)); + d.setDevice(prepareDatasetDevice(doc, info)); + d.setSize(prepareDatasetSize(doc, info)); + d.setVersion(prepareDatasetVersion(doc, info)); + d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); + d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); + d.setGeolocation(prepareDatasetGeoLocations(doc, info)); + oafs.add(d); + break; + case "software": + final Software s = new Software(); + populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER); + s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); + s.setLicense(prepareSoftwareLicenses(doc, info)); + s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); + s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); + oafs.add(s); + break; + case "otherresearchproducts": + default: + final OtherResearchProduct o = new OtherResearchProduct(); + populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp); + o.setResulttype(OTHER_RESULTTYPE_QUALIFIER); + o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); + o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); + o.setTool(prepareOtherResearchProductTools(doc, info)); + oafs.add(o); + break; + } + + if (!oafs.isEmpty()) { + oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); + oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); + } + + return oafs; + } + + private List addProjectRels(final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + + final List res = new ArrayList<>(); + + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier")); + + for (final Object o : doc.selectNodes("//oaf:projectid")) { + final String projectId = createOpenaireId(40, ((Node) o).getText()); + + final Relation r1 = new Relation(); + r1.setRelType("resultProject"); + r1.setSubRelType("outcome"); + r1.setRelClass("isProducedBy"); + r1.setSource(docId); + r1.setTarget(projectId); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); + + final Relation r2 = new Relation(); + r2.setRelType("resultProject"); + r2.setSubRelType("outcome"); + r2.setRelClass("produces"); + r2.setSource(projectId); + r2.setTarget(docId); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + + return res; + } + + protected abstract List addOtherResultRels(final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp); + + private void populateResultFields(final Result r, + final Document doc, + final KeyValue collectedFrom, + final KeyValue hostedBy, + final DataInfo info, + final long lastUpdateTimestamp) { + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"))); + r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier"))); + r.setCollectedfrom(Arrays.asList(collectedFrom)); + r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info)); + r.setDateofcollection(doc.valueOf("//dr:dateOfCollection")); + r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation")); + r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setOaiprovenance(prepareOAIprovenance(doc)); + r.setAuthor(prepareAuthors(doc, info)); + r.setLanguage(prepareLanguages(doc)); + r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setSubject(prepareSubjects(doc, info)); + r.setTitle(prepareTitles(doc, info)); + r.setRelevantdate(prepareRelevantDates(doc, info)); + r.setDescription(prepareDescriptions(doc, info)); + r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info)); + r.setPublisher(preparePublisher(doc, info)); + r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); + r.setSource(prepareSources(doc, info)); + r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFormat(prepareFormats(doc, info)); + r.setContributor(prepareContributors(doc, info)); + r.setResourcetype(prepareResourceType(doc, info)); + r.setCoverage(prepareCoverages(doc, info)); + r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy)); + } + + protected abstract Qualifier prepareResourceType(Document doc, DataInfo info); + + protected abstract List prepareInstances(Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby); + + protected abstract List> prepareSources(Document doc, DataInfo info); + + protected abstract List prepareRelevantDates(Document doc, DataInfo info); + + protected abstract List> prepareCoverages(Document doc, DataInfo info); + + protected abstract List> prepareContributors(Document doc, DataInfo info); + + protected abstract List> prepareFormats(Document doc, DataInfo info); + + protected abstract Field preparePublisher(Document doc, DataInfo info); + + protected abstract List> prepareDescriptions(Document doc, DataInfo info); + + protected abstract List prepareTitles(Document doc, DataInfo info); + + protected abstract List prepareSubjects(Document doc, DataInfo info); + + protected abstract Qualifier prepareLanguages(Document doc); + + protected abstract List prepareAuthors(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductTools(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactGroups(Document doc, DataInfo info); + + protected abstract List> prepareOtherResearchProductContactPersons(Document doc, DataInfo info); + + protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info); + + protected abstract Field prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info); + + protected abstract List prepareSoftwareLicenses(Document doc, DataInfo info); + + protected abstract List> prepareSoftwareDocumentationUrls(Document doc, DataInfo info); + + protected abstract List prepareDatasetGeoLocations(Document doc, DataInfo info); + + protected abstract Field prepareDatasetMetadataVersionNumber(Document doc, DataInfo info); + + protected abstract Field prepareDatasetLastMetadataUpdate(Document doc, DataInfo info); + + protected abstract Field prepareDatasetVersion(Document doc, DataInfo info); + + protected abstract Field prepareDatasetSize(Document doc, DataInfo info); + + protected abstract Field prepareDatasetDevice(Document doc, DataInfo info); + + protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); + + private Journal prepareJournal(final Document doc, final DataInfo info) { + final Node n = doc.selectSingleNode("//oaf:journal"); + if (n != null) { + final String name = n.getText(); + final String issnPrinted = n.valueOf("@issn"); + final String issnOnline = n.valueOf("@eissn"); + final String issnLinking = n.valueOf("@lissn"); + final String ep = n.valueOf("@ep"); + final String iss = n.valueOf("@iss"); + final String sp = n.valueOf("@sp"); + final String vol = n.valueOf("@vol"); + final String edition = n.valueOf("@edition"); + if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); } + } + return null; + } + + protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId, final String schemeName) { + final String classId = node.valueOf(xpath); + final String className = code2name.get(classId); + return qualifier(classId, className, schemeId, schemeName); + } + + protected List prepareListStructProps(final Node node, + final String xpath, + final String xpathClassId, + final String schemeId, + final String schemeName, + final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + final String classId = n.valueOf(xpathClassId); + final String className = code2name.get(classId); + res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info)); + } + return res; + } + + protected List prepareListStructProps(final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), qualifier, info)); + } + return res; + } + + protected List prepareListStructProps(final Node node, final String xpath, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final Node n = (Node) o; + res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n + .valueOf("@schemename"), info)); + } + return res; + } + + protected OAIProvenance prepareOAIprovenance(final Document doc) { + final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']"); + + if (n == null) { return null; } + + final String identifier = n.valueOf("./*[local-name()='identifier']"); + final String baseURL = n.valueOf("./*[local-name()='baseURL']");; + final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");; + final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true"); + final String datestamp = n.valueOf("./*[local-name()='datestamp']");; + final String harvestDate = n.valueOf("@harvestDate");; + + return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate); + + } + + protected DataInfo prepareDataInfo(final Document doc) { + final Node n = doc.selectSingleNode("//oaf:datainfo"); + + final String paClassId = n.valueOf("./oaf:provenanceaction/@classid"); + final String paClassName = n.valueOf("./oaf:provenanceaction/@classname"); + final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid"); + final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename"); + + final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference")); + final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance"); + final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred")); + final String trust = n.valueOf("./oaf:trust"); + + return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust); + } + + protected Field prepareField(final Node node, final String xpath, final DataInfo info) { + return field(node.valueOf(xpath), info); + } + + protected List> prepareListFields(final Node node, final String xpath, final DataInfo info) { + return listFields(info, prepareListString(node, xpath)); + } + + protected List prepareListString(final Node node, final String xpath) { + final List res = new ArrayList<>(); + for (final Object o : node.selectNodes(xpath)) { + final String s = ((Node) o).getText().trim(); + if (StringUtils.isNotBlank(s)) { + res.add(s); + } + } + return res; + } + + @Override + public void close() throws IOException { + super.close(); + mdstoreClient.close(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/DbClient.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/DbClient.java new file mode 100644 index 000000000..9ac0089d2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/DbClient.java @@ -0,0 +1,63 @@ +package eu.dnetlib.dhp.migration; + +import java.io.Closeable; +import java.io.IOException; +import java.sql.Connection; +import java.sql.DriverManager; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.function.Consumer; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +public class DbClient implements Closeable { + + private static final Log log = LogFactory.getLog(DbClient.class); + + private Connection connection; + + public DbClient(final String address, final String login, final String password) { + + try { + Class.forName("org.postgresql.Driver"); + + this.connection = + StringUtils.isNoneBlank(login, password) ? DriverManager.getConnection(address, login, password) : DriverManager.getConnection(address); + this.connection.setAutoCommit(false); + } catch (final Exception e) { + log.error(e.getClass().getName() + ": " + e.getMessage()); + throw new RuntimeException(e); + } + log.info("Opened database successfully"); + } + + public void processResults(final String sql, final Consumer consumer) { + + try (final Statement stmt = connection.createStatement()) { + stmt.setFetchSize(100); + + try (final ResultSet rs = stmt.executeQuery(sql)) { + while (rs.next()) { + consumer.accept(rs); + } + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } catch (final SQLException e1) { + throw new RuntimeException(e1); + } + } + + @Override + public void close() throws IOException { + try { + connection.close(); + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java new file mode 100644 index 000000000..f2d9caebf --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/ExtractEntitiesFromHDFSJob.java @@ -0,0 +1,56 @@ +package eu.dnetlib.dhp.migration; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import scala.Tuple2; + +import java.util.Arrays; +import java.util.List; + +public class ExtractEntitiesFromHDFSJob { + + + private static List folderNames = Arrays.asList("db_entities", "oaf_entities", "odf_entities"); + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json"))); + parser.parseArgument(args); + + final SparkSession spark = SparkSession + .builder() + .appName(ExtractEntitiesFromHDFSJob.class.getSimpleName()) + .master(parser.get("master")) + .getOrCreate(); + + final String sourcePath = parser.get("sourcePath"); + final String targetPath = parser.get("graphRawPath"); + final String entity = parser.get("entity"); + + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + + JavaRDD inputRdd = sc.emptyRDD(); + + + folderNames.forEach(p -> inputRdd.union( + sc.sequenceFile(sourcePath+"/"+p, Text.class, Text.class) + .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) + .filter(k -> isEntityType(k._1(), entity)) + .map(Tuple2::_2)) + ); + + inputRdd.saveAsTextFile(targetPath+"/"+entity); + } + + + private static boolean isEntityType(final String item, final String entity) { + return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MdstoreClient.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MdstoreClient.java new file mode 100644 index 000000000..87dadfc7a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MdstoreClient.java @@ -0,0 +1,94 @@ +package eu.dnetlib.dhp.migration; + +import java.io.Closeable; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Map; +import java.util.stream.StreamSupport; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.bson.Document; + +import com.google.common.collect.Iterables; +import com.mongodb.MongoClient; +import com.mongodb.MongoClientURI; +import com.mongodb.client.MongoCollection; +import com.mongodb.client.MongoDatabase; + +public class MdstoreClient implements Closeable { + + private final MongoClient client; + private final MongoDatabase db; + + private static final String COLL_METADATA = "metadata"; + private static final String COLL_METADATA_MANAGER = "metadataManager"; + + private static final Log log = LogFactory.getLog(MdstoreClient.class); + + public MdstoreClient(final String baseUrl, final String dbName) { + this.client = new MongoClient(new MongoClientURI(baseUrl)); + this.db = getDb(client, dbName); + } + + public Map validCollections(final String mdFormat, final String mdLayout, final String mdInterpretation) { + + final Map transactions = new HashMap<>(); + for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) { + final String mdId = entry.getString("mdId"); + final String currentId = entry.getString("currentId"); + if (StringUtils.isNoneBlank(mdId, currentId)) { + transactions.put(mdId, currentId); + } + } + + final Map res = new HashMap<>(); + for (final Document entry : getColl(db, COLL_METADATA, true).find()) { + if (entry.getString("format").equals(mdFormat) && entry.getString("layout").equals(mdLayout) + && entry.getString("interpretation").equals(mdInterpretation) && transactions.containsKey(entry.getString("mdId"))) { + res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId"))); + } + } + + return res; + } + + private MongoDatabase getDb(final MongoClient client, final String dbName) { + if (!Iterables.contains(client.listDatabaseNames(), dbName)) { + final String err = String.format("Database '%s' not found in %s", dbName, client.getAddress()); + log.warn(err); + throw new RuntimeException(err); + } + return client.getDatabase(dbName); + } + + private MongoCollection getColl(final MongoDatabase db, final String collName, final boolean abortIfMissing) { + if (!Iterables.contains(db.listCollectionNames(), collName)) { + final String err = String.format(String.format("Missing collection '%s' in database '%s'", collName, db.getName())); + log.warn(err); + if (abortIfMissing) { + throw new RuntimeException(err); + } else { + return null; + } + } + return db.getCollection(collName); + } + + public Iterable listRecords(final String collName) { + final MongoCollection coll = getColl(db, collName, false); + return coll == null ? new ArrayList<>() + : () -> StreamSupport.stream(coll.find().spliterator(), false) + .filter(e -> e.containsKey("body")) + .map(e -> e.getString("body")) + .iterator(); + } + + @Override + public void close() throws IOException { + client.close(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java new file mode 100644 index 000000000..d22e8e5b3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateDbEntitiesApplication.java @@ -0,0 +1,520 @@ +package eu.dnetlib.dhp.migration; + +import java.io.Closeable; +import java.io.IOException; +import java.sql.Array; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Date; +import java.util.List; +import java.util.function.Consumer; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor implements Closeable { + + private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION = + qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions"); + + private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class); + + private final DbClient dbClient; + + private final long lastUpdateTimestamp; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("namenode"); + final String hdfsUser = parser.get("hdfsUser"); + + try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) { + log.info("Processing datasources..."); + smdbe.execute("queryDatasources.sql", smdbe::processDatasource); + + log.info("Processing projects..."); + smdbe.execute("queryProjects.sql", smdbe::processProject); + + log.info("Processing orgs..."); + smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); + + log.info("Processing relations ds <-> orgs ..."); + smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); + + log.info("Processing projects <-> orgs ..."); + smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); + + log.info("All done."); + } + } + + public MigrateDbEntitiesApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String dbUrl, final String dbUser, + final String dbPassword) throws Exception { + super(hdfsPath, hdfsNameNode, hdfsUser); + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + this.lastUpdateTimestamp = new Date().getTime(); + } + + public void execute(final String sqlFile, final Consumer consumer) throws Exception { + final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/migration/sql/" + sqlFile)); + dbClient.processResults(sql, consumer); + } + + public void processDatasource(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Datasource ds = new Datasource(); + + ds.setId(createOpenaireId(10, rs.getString("datasourceid"))); + ds.setOriginalId(Arrays.asList(rs.getString("datasourceid"))); + ds.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + ds.setPid(new ArrayList<>()); + ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); + ds.setDateoftransformation(null); // Value not returned by the SQL query + ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB + ds.setOaiprovenance(null); // Values not present in the DB + ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); + ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); + ds.setOfficialname(field(rs.getString("officialname"), info)); + ds.setEnglishname(field(rs.getString("englishname"), info)); + ds.setWebsiteurl(field(rs.getString("websiteurl"), info)); + ds.setLogourl(field(rs.getString("logourl"), info)); + ds.setContactemail(field(rs.getString("contactemail"), info)); + ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info)); + ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info)); + ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info)); + ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info)); + ds.setDescription(field(rs.getString("description"), info)); + ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info)); + ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); + ds.setOdpolicies(field(rs.getString("odpolicies"), info)); + ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); + ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); + ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); + ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); + ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); + ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); + ds.setDataprovider(field(rs.getBoolean("dataprovider"), info)); + ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info)); + ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); + ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); + ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); + ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); + ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); + ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); + ds.setCertificates(field(rs.getString("certificates"), info)); + ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array + ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal + ds.setDataInfo(info); + ds.setLastupdatetimestamp(lastUpdateTimestamp); + + // rs.getString("datasourceid"); + // rs.getArray("identities"); + // rs.getString("officialname"); + // rs.getString("englishname"); + // rs.getString("contactemail"); + // rs.getString("openairecompatibility"); // COMPLEX ...@@@... + // rs.getString("websiteurl"); + // rs.getString("logourl"); + // rs.getArray("accessinfopackage"); + // rs.getDouble("latitude"); + // rs.getDouble("longitude"); + // rs.getString("namespaceprefix"); + // rs.getInt("odnumberofitems"); // NULL + // rs.getDate("odnumberofitemsdate"); // NULL + // rs.getArray("subjects"); + // rs.getString("description"); + // rs.getString("odpolicies"); // NULL + // rs.getArray("odlanguages"); + // rs.getArray("odcontenttypes"); + // rs.getBoolean("inferred"); // false + // rs.getBoolean("deletedbyinference");// false + // rs.getDouble("trust"); // 0.9 + // rs.getString("inferenceprovenance"); // NULL + // rs.getDate("dateofcollection"); + // rs.getDate("dateofvalidation"); + // rs.getDate("releasestartdate"); + // rs.getDate("releaseenddate"); + // rs.getString("missionstatementurl"); + // rs.getBoolean("dataprovider"); + // rs.getBoolean("serviceprovider"); + // rs.getString("databaseaccesstype"); + // rs.getString("datauploadtype"); + // rs.getString("databaseaccessrestriction"); + // rs.getString("datauploadrestriction"); + // rs.getBoolean("versioning"); + // rs.getString("citationguidelineurl"); + // rs.getString("qualitymanagementkind"); + // rs.getString("pidsystems"); + // rs.getString("certificates"); + // rs.getArray("policies"); + // rs.getString("collectedfromid"); + // rs.getString("collectedfromname"); + // rs.getString("datasourcetype"); // COMPLEX + // rs.getString("provenanceaction"); // + // 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' + // AS provenanceaction, + // rs.getString("journal"); // CONCAT(d.issn, '@@@', d.eissn, '@@@', d.lissn) AS journal + + emitOaf(ds); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public void processProject(final ResultSet rs) { + try { + + final DataInfo info = prepareDataInfo(rs); + + final Project p = new Project(); + + p.setId(createOpenaireId(40, rs.getString("projectid"))); + p.setOriginalId(Arrays.asList(rs.getString("projectid"))); + p.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + p.setPid(new ArrayList<>()); + p.setDateofcollection(asString(rs.getDate("dateofcollection"))); + p.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); + p.setExtraInfo(new ArrayList<>()); // Values not present in the DB + p.setOaiprovenance(null); // Values not present in the DB + p.setWebsiteurl(field(rs.getString("websiteurl"), info)); + p.setCode(field(rs.getString("code"), info)); + p.setAcronym(field(rs.getString("acronym"), info)); + p.setTitle(field(rs.getString("title"), info)); + p.setStartdate(field(asString(rs.getDate("startdate")), info)); + p.setEnddate(field(asString(rs.getDate("enddate")), info)); + p.setCallidentifier(field(rs.getString("callidentifier"), info)); + p.setKeywords(field(rs.getString("keywords"), info)); + p.setDuration(field(Integer.toString(rs.getInt("duration")), info)); + p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info)); + p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info)); + p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info)); + p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info)); + p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info)); + p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype"))); + p.setOptional1(field(rs.getString("optional1"), info)); + p.setOptional2(field(rs.getString("optional2"), info)); + p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info)); + p.setContactfullname(field(rs.getString("contactfullname"), info)); + p.setContactfax(field(rs.getString("contactfax"), info)); + p.setContactphone(field(rs.getString("contactphone"), info)); + p.setContactemail(field(rs.getString("contactemail"), info)); + p.setSummary(field(rs.getString("summary"), info)); + p.setCurrency(field(rs.getString("currency"), info)); + p.setTotalcost(new Float(rs.getDouble("totalcost"))); + p.setFundedamount(new Float(rs.getDouble("fundedamount"))); + p.setDataInfo(info); + p.setLastupdatetimestamp(lastUpdateTimestamp); + + // rs.getString("projectid"); + // rs.getString("code"); + // rs.getString("websiteurl"); + // rs.getString("acronym"); + // rs.getString("title"); + // rs.getDate("startdate"); + // rs.getDate("enddate"); + // rs.getString("callidentifier"); + // rs.getString("keywords"); + // rs.getInt("duration"); + // rs.getBoolean("ecsc39"); + // rs.getBoolean("oamandatepublications"); + // rs.getBoolean("ecarticle29_3"); + // rs.getDate("dateofcollection"); + // rs.getDate("dateoftransformation"); + // rs.getBoolean("inferred"); + // rs.getBoolean("deletedbyinference"); + // rs.getDouble("trust"); + // rs.getString("inferenceprovenance"); + // rs.getString("optional1"); + // rs.getString("optional2"); + // rs.getString("jsonextrainfo"); + // rs.getString("contactfullname"); + // rs.getString("contactfax"); + // rs.getString("contactphone"); + // rs.getString("contactemail"); + // rs.getString("summary"); + // rs.getString("currency"); + // rs.getDouble("totalcost"); + // rs.getDouble("fundedamount"); + // rs.getString("collectedfromid"); + // rs.getString("collectedfromname"); + // rs.getString("contracttype"); // COMPLEX + // rs.getString("provenanceaction"); // COMPLEX + // rs.getArray("pid"); + // rs.getArray("subjects"); + // rs.getArray("fundingtree"); + + emitOaf(p); + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public void processOrganization(final ResultSet rs) { + + try { + + final DataInfo info = prepareDataInfo(rs); + + final Organization o = new Organization(); + + o.setId(createOpenaireId(20, rs.getString("organizationid"))); + o.setOriginalId(Arrays.asList(rs.getString("organizationid"))); + o.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"))); + o.setPid(new ArrayList<>()); + o.setDateofcollection(asString(rs.getDate("dateofcollection"))); + o.setDateoftransformation(asString(rs.getDate("dateoftransformation"))); + o.setExtraInfo(new ArrayList<>()); // Values not present in the DB + o.setOaiprovenance(null); // Values not present in the DB + o.setLegalshortname(field("legalshortname", info)); + o.setLegalname(field("legalname", info)); + o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query + o.setWebsiteurl(field("websiteurl", info)); + o.setLogourl(field("logourl", info)); + o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info)); + o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info)); + o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info)); + o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info)); + o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info)); + o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info)); + o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info)); + o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info)); + o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info)); + o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info)); + o.setCountry(prepareQualifierSplitting(rs.getString("country"))); + o.setDataInfo(info); + o.setLastupdatetimestamp(lastUpdateTimestamp); + + // rs.getString("organizationid"); + // rs.getString("legalshortname"); + // rs.getString("legalname"); + // rs.getString("websiteurl"); + // rs.getString("logourl"); + // rs.getBoolean("eclegalbody"); + // rs.getBoolean("eclegalperson"); + // rs.getBoolean("ecnonprofit"); + // rs.getBoolean("ecresearchorganization"); + // rs.getBoolean("echighereducation"); + // rs.getBoolean("ecinternationalorganizationeurinterests"); + // rs.getBoolean("ecinternationalorganization"); + // rs.getBoolean("ecenterprise"); + // rs.getBoolean("ecsmevalidated"); + // rs.getBoolean("ecnutscode"); + // rs.getDate("dateofcollection"); + // rs.getDate("dateoftransformation"); + // rs.getBoolean("inferred"); + // rs.getBoolean("deletedbyinference"); + // rs.getDouble("trust"); + // rs.getString("inferenceprovenance"); + // rs.getString("collectedfromid"); + // rs.getString("collectedfromname"); + // rs.getString("country"); + // rs.getString("provenanceaction"); + // rs.getArray("pid"); + + emitOaf(o); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public void processDatasourceOrganization(final ResultSet rs) { + + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("organization")); + final String dsId = createOpenaireId(10, rs.getString("datasource")); + final List collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("datasourceOrganization"); + r1.setSubRelType("provision"); + r1.setRelClass("isProvidedBy"); + r1.setSource(dsId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + emitOaf(r1); + + final Relation r2 = new Relation(); + r2.setRelType("datasourceOrganization"); + r2.setSubRelType("provision"); + r2.setRelClass("provides"); + r2.setSource(orgId); + r2.setTarget(dsId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + emitOaf(r2); + + // rs.getString("datasource"); + // rs.getString("organization"); + // rs.getDate("startdate"); // NULL + // rs.getDate("enddate"); // NULL + // rs.getBoolean("inferred"); // false + // rs.getBoolean("deletedbyinference"); // false + // rs.getDouble("trust"); // 0.9 + // rs.getString("inferenceprovenance"); // NULL + // rs.getString("semantics"); // 'providedBy@@@provided + // by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS + // semantics, + // rs.getString("provenanceaction"); // d.provenanceaction || '@@@' || d.provenanceaction || + // '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public void processProjectOrganization(final ResultSet rs) { + + try { + final DataInfo info = prepareDataInfo(rs); + final String orgId = createOpenaireId(20, rs.getString("resporganization")); + final String projectId = createOpenaireId(40, rs.getString("project")); + final List collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")); + + final Relation r1 = new Relation(); + r1.setRelType("projectOrganization"); + r1.setSubRelType("participation"); + r1.setRelClass("isParticipant"); + r1.setSource(projectId); + r1.setTarget(orgId); + r1.setCollectedFrom(collectedFrom); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + emitOaf(r1); + + final Relation r2 = new Relation(); + r2.setRelType("projectOrganization"); + r2.setSubRelType("participation"); + r2.setRelClass("hasParticipant"); + r2.setSource(orgId); + r2.setTarget(projectId); + r2.setCollectedFrom(collectedFrom); + r2.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + emitOaf(r2); + + // rs.getString("project"); + // rs.getString("resporganization"); + // rs.getInt("participantnumber"); + // rs.getDouble("contribution"); + // rs.getDate("startdate");// null + // rs.getDate("enddate");// null + // rs.getBoolean("inferred");// false + // rs.getBoolean("deletedbyinference"); // false + // rs.getDouble("trust"); + // rs.getString("inferenceprovenance"); // NULL + // rs.getString("semantics"); // po.semanticclass || '@@@' || po.semanticclass || + // '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics, + // rs.getString("provenanceaction"); // + // 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' + // AS provenanceaction + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException { + final Boolean deletedbyinference = rs.getBoolean("deletedbyinference"); + final String inferenceprovenance = rs.getString("inferenceprovenance"); + final Boolean inferred = rs.getBoolean("inferred"); + final String trust = rs.getString("trust"); + return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust); + } + + private Qualifier prepareQualifierSplitting(final String s) { + if (StringUtils.isBlank(s)) { return null; } + final String[] arr = s.split("@@@"); + return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null; + } + + private List> prepareListFields(final Array array, final DataInfo info) { + try { + return listFields(info, (String[]) array.getArray()); + } catch (final SQLException e) { + throw new RuntimeException("Invalid SQL array", e); + } + } + + private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) { + if (StringUtils.isBlank(s)) { return null; } + final String[] parts = s.split("###"); + if (parts.length == 2) { + final String value = parts[0]; + final String[] arr = parts[1].split("@@@"); + if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); } + } + return null; + } + + private List prepareListOfStructProps(final Array array, final DataInfo dataInfo) throws SQLException { + final List res = new ArrayList<>(); + if (array != null) { + for (final String s : (String[]) array.getArray()) { + final StructuredProperty sp = prepareStructProp(s, dataInfo); + if (sp != null) { + res.add(sp); + } + } + } + + return res; + } + + private Journal prepareJournal(final String name, final String sj, final DataInfo info) { + if (StringUtils.isNotBlank(sj)) { + final String[] arr = sj.split("@@@"); + if (arr.length == 3) { + final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null; + final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;; + final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;; + if (issn != null || eissn != null + || lissn != null) { return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); } + } + } + return null; + } + + @Override + public void close() throws IOException { + super.close(); + dbClient.close(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateMongoMdstoresApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateMongoMdstoresApplication.java new file mode 100644 index 000000000..359fe7596 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MigrateMongoMdstoresApplication.java @@ -0,0 +1,45 @@ +package eu.dnetlib.dhp.migration; + +import org.apache.commons.io.IOUtils; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class MigrateMongoMdstoresApplication { + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json"))); + parser.parseArgument(args); + + final String mongoBaseUrl = parser.get("mongoBaseUrl"); + final String mongoDb = parser.get("mongoDb"); + + final String mdFormat = parser.get("mdFormat"); + final String mdLayout = parser.get("mdLayout"); + final String mdInterpretation = parser.get("mdInterpretation"); + + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("namenode"); + final String hdfsUser = parser.get("hdfsUser"); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + + if (mdFormat.equalsIgnoreCase("oaf")) { + try (final OafMigrationExecutor mig = + new OafMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) { + mig.processMdRecords(mdFormat, mdLayout, mdInterpretation); + } + } else if (mdFormat.equalsIgnoreCase("odf")) { + try (final OdfMigrationExecutor mig = + new OdfMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) { + mig.processMdRecords(mdFormat, mdLayout, mdInterpretation); + } + } else { + throw new RuntimeException("Format not supported: " + mdFormat); + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java new file mode 100644 index 000000000..c32568290 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OafMigrationExecutor.java @@ -0,0 +1,251 @@ +package eu.dnetlib.dhp.migration; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.dom4j.Document; +import org.dom4j.Node; + +import eu.dnetlib.dhp.migration.pace.PacePerson; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class OafMigrationExecutor extends AbstractMongoExecutor { + + private static final Log log = LogFactory.getLog(OafMigrationExecutor.class); + + public OafMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb, + final String dbUrl, final String dbUser, + final String dbPassword) throws Exception { + super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword); + } + + @Override + protected void registerNamespaces(final Map nsContext) { + super.registerNamespaces(nsContext); + nsContext.put("dc", "http://purl.org/dc/elements/1.1/"); + } + + @Override + protected List prepareAuthors(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + int pos = 1; + for (final Object o : doc.selectNodes("//dc:creator")) { + final Node n = (Node) o; + final Author author = new Author(); + author.setFullname(n.getText()); + author.setRank(pos++); + final PacePerson p = new PacePerson(n.getText(), false); + if (p.isAccurate()) { + author.setName(p.getNormalisedFirstName()); + author.setSurname(p.getNormalisedSurname()); + } + res.add(author); + } + return res; + } + + @Override + protected Qualifier prepareLanguages(final Document doc) { + return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages"); + } + + @Override + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:subject", info); + } + + @Override + protected List prepareTitles(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info); + } + + @Override + protected List> prepareDescriptions(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:description", info); + } + + @Override + protected Field preparePublisher(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:publisher", info); + } + + @Override + protected List> prepareFormats(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:format", info); + } + + @Override + protected List> prepareContributors(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:contributor", info); + } + + @Override + protected List> prepareCoverages(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:coverage", info); + } + + @Override + protected List prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("//dc:identifier")) { + final String url = ((Node) o).getText().trim(); + if (url.startsWith("http")) { + final Instance instance = new Instance(); + instance.setUrl(Arrays.asList(url)); + instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource")); + instance.setCollectedfrom(collectedfrom); + instance.setHostedby(hostedby); + instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); + instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); + instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); + instance.setLicense(field(doc.valueOf("//oaf:license"), info)); + instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); + instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + res.add(instance); + } + } + return res; + } + + @Override + protected List> prepareSources(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:source", info); + } + + @Override + protected List prepareRelevantDates(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + // SOFTWARES + + @Override + protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected List prepareSoftwareLicenses(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + @Override + protected List> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + // DATASETS + @Override + protected List prepareDatasetGeoLocations(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetSize(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + @Override + protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + + // OTHER PRODUCTS + + @Override + protected List> prepareOtherResearchProductTools(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + @Override + protected List> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + @Override + protected List> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) { + return new ArrayList<>(); // NOT PRESENT IN OAF + } + + @Override + protected List addOtherResultRels(final Document doc, + final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp) { + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier")); + + final List res = new ArrayList<>(); + + for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) { + final String otherId = createOpenaireId(50, ((Node) o).getText()); + + final Relation r1 = new Relation(); + r1.setRelType("resultResult"); + r1.setSubRelType("publicationDataset"); + r1.setRelClass("isRelatedTo"); + r1.setSource(docId); + r1.setTarget(otherId); + r1.setCollectedFrom(Arrays.asList(collectedFrom)); + r1.setDataInfo(info); + r1.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r1); + + final Relation r2 = new Relation(); + r2.setRelType("resultResult"); + r2.setSubRelType("publicationDataset"); + r2.setRelClass("isRelatedTo"); + r2.setSource(otherId); + r2.setTarget(docId); + r2.setCollectedFrom(Arrays.asList(collectedFrom)); + r2.setDataInfo(info); + r2.setLastupdatetimestamp(lastUpdateTimestamp); + res.add(r2); + } + return res; + } + + @Override + protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { + return null; // NOT PRESENT IN OAF + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java new file mode 100644 index 000000000..457534085 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java @@ -0,0 +1,273 @@ +package eu.dnetlib.dhp.migration; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.dom4j.Document; +import org.dom4j.Node; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class OdfMigrationExecutor extends AbstractMongoExecutor { + + private static final Log log = LogFactory.getLog(OdfMigrationExecutor.class); + + public OdfMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb, + final String dbUrl, final String dbUser, + final String dbPassword) throws Exception { + super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword); + } + + @Override + protected void registerNamespaces(final Map nsContext) { + super.registerNamespaces(nsContext); + nsContext.put("dc", "http://datacite.org/schema/kernel-3"); + } + + @Override + protected List prepareTitles(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info); + } + + @Override + protected List prepareAuthors(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + int pos = 1; + for (final Object o : doc.selectNodes("//dc:creator")) { + final Node n = (Node) o; + final Author author = new Author(); + author.setFullname(n.valueOf("./dc:creatorName")); + author.setName(n.valueOf("./dc:givenName")); + author.setSurname(n.valueOf("./dc:familyName")); + author.setAffiliation(prepareListFields(doc, "./dc:affiliation", info)); + author.setPid(preparePids(doc, info)); + author.setRank(pos++); + res.add(author); + } + return res; + } + + private List preparePids(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("./dc:nameIdentifier")) { + res.add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", "dnet:pid_types", "dnet:pid_types"), info)); + } + return res; + } + + @Override + protected List prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("//dc:alternateIdentifier[@alternateIdentifierType='URL']")) { + final Instance instance = new Instance(); + instance.setUrl(Arrays.asList(((Node) o).getText().trim())); + instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource")); + instance.setCollectedfrom(collectedfrom); + instance.setHostedby(hostedby); + instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info)); + instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation")); + instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes")); + instance.setLicense(field(doc.valueOf("//oaf:license"), info)); + instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info)); + instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info)); + instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info)); + res.add(instance); + } + return res; + } + + @Override + protected List> prepareSources(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } + + @Override + protected List prepareRelevantDates(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + for (final Object o : doc.selectNodes("//dc:date")) { + final String dateType = ((Node) o).valueOf("@dateType"); + if (StringUtils.isBlank(dateType) && !dateType.equalsIgnoreCase("Accepted") && !dateType.equalsIgnoreCase("Issued") + && !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) { + res.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", "dnet:dataCite_date", "dnet:dataCite_date", info)); + } + } + return res; + } + + @Override + protected List> prepareCoverages(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } + + @Override + protected List> prepareContributors(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:contributorName", info); + } + + @Override + protected List> prepareFormats(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:format", info); + } + + @Override + protected Field preparePublisher(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:publisher", info); + } + + @Override + protected List> prepareDescriptions(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:description[@descriptionType='Abstract']", info); + } + + @Override + protected List prepareSubjects(final Document doc, final DataInfo info) { + return prepareListStructProps(doc, "//dc:subject", info); + } + + @Override + protected Qualifier prepareLanguages(final Document doc) { + return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages"); + } + + @Override + protected List> prepareOtherResearchProductTools(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } + + @Override + protected List> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:contributor[@contributorType='ContactGroup']/dc:contributorName", info); + } + + @Override + protected List> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:contributor[@contributorType='ContactPerson']/dc:contributorName", info); + } + + @Override + protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) { + return prepareQualifier(doc, "//dc:format", "dnet:programming_languages", "dnet:programming_languages"); + } + + @Override + protected Field prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } + + @Override + protected List prepareSoftwareLicenses(final Document doc, final DataInfo info) { + return new ArrayList<>(); // Not present in ODF ??? + } + + @Override + protected List> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) { + return prepareListFields(doc, "//dc:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info); + } + + // DATASETS + + @Override + protected List prepareDatasetGeoLocations(final Document doc, final DataInfo info) { + final List res = new ArrayList<>(); + + for (final Object o : doc.selectNodes("//dc:geoLocation")) { + final GeoLocation loc = new GeoLocation(); + loc.setBox(((Node) o).valueOf("./dc:geoLocationBox")); + loc.setPlace(((Node) o).valueOf("./dc:geoLocationPlace")); + loc.setPoint(((Node) o).valueOf("./dc:geoLocationPoint")); + res.add(loc); + } + return res; + } + + @Override + protected Field prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } + + @Override + protected Field prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:date[@dateType='Updated']", info); + } + + @Override + protected Field prepareDatasetVersion(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:version", info); + } + + @Override + protected Field prepareDatasetSize(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:size", info); + } + + @Override + protected Field prepareDatasetDevice(final Document doc, final DataInfo info) { + return null; // Not present in ODF ??? + } + + @Override + protected Field prepareDatasetStorageDate(final Document doc, final DataInfo info) { + return prepareField(doc, "//dc:date[@dateType='Issued']", info); + } + + @Override + protected List addOtherResultRels(final Document doc, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) { + + final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier")); + + final List res = new ArrayList<>(); + + for (final Object o : doc.selectNodes("//*[local-name() = 'resource']//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) { + final String otherId = createOpenaireId(50, ((Node) o).getText()); + final String type = ((Node) o).valueOf("@relationType"); + + if (type.equals("IsSupplementTo")) { + res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "supplement", "isSupplementTo")); + res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "supplement", "isSupplementedBy")); + } else if (type.equals("IsPartOf")) { + res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf")); + res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts")); + } else {} + } + return res; + } + + private Relation prepareOtherResultRel(final KeyValue collectedFrom, + final DataInfo info, + final long lastUpdateTimestamp, + final String source, + final String target, + final String subRelType, + final String relClass) { + final Relation r = new Relation(); + r.setRelType("resultResult"); + r.setSubRelType(subRelType); + r.setRelClass(relClass); + r.setSource(source); + r.setTarget(target); + r.setCollectedFrom(Arrays.asList(collectedFrom)); + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + return r; + } + + @Override + protected Qualifier prepareResourceType(final Document doc, final DataInfo info) { + return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", "dnet:dataCite_resource", "dnet:dataCite_resource"); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/pace/PacePerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/pace/PacePerson.java new file mode 100644 index 000000000..927f5641b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/pace/PacePerson.java @@ -0,0 +1,176 @@ +package eu.dnetlib.dhp.migration.pace; + +import java.nio.charset.Charset; +import java.text.Normalizer; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.text.WordUtils; + +import com.google.common.base.Joiner; +import com.google.common.base.Splitter; +import com.google.common.collect.Iterables; +import com.google.common.collect.Lists; +import com.google.common.hash.Hashing; + +public class PacePerson { + + private static final String UTF8 = "UTF-8"; + private List name = Lists.newArrayList(); + private List surname = Lists.newArrayList(); + private List fullname = Lists.newArrayList(); + private final String original; + + private static Set particles = null; + + public static final String capitalize(final String s) { + return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); + } + + public static final String dotAbbreviations(final String s) { + return s.length() == 1 ? s + "." : s; + } + + public static Set loadFromClasspath(final String classpath) { + final Set h = new HashSet<>(); + try { + for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) { + h.add(s); + } + } catch (final Throwable e) { + return new HashSet<>(); + } + return h; + } + + public PacePerson(String s, final boolean aggressive) { + original = s; + s = Normalizer.normalize(s, Normalizer.Form.NFD); + s = s.replaceAll("\\(.+\\)", ""); + s = s.replaceAll("\\[.+\\]", ""); + s = s.replaceAll("\\{.+\\}", ""); + s = s.replaceAll("\\s+-\\s+", "-"); + s = s.replaceAll("[\\p{Punct}&&[^,-]]", " "); + s = s.replaceAll("\\d", " "); + s = s.replaceAll("\\n", " "); + s = s.replaceAll("\\.", " "); + s = s.replaceAll("\\s+", " "); + + if (aggressive) { + s = s.replaceAll("[\\p{InCombiningDiacriticalMarks}&&[^,-]]", ""); + // s = s.replaceAll("[\\W&&[^,-]]", ""); + } + + if (s.contains(",")) { + final String[] arr = s.split(","); + if (arr.length == 1) { + fullname = splitTerms(arr[0]); + } else if (arr.length > 1) { + surname = splitTerms(arr[0]); + name = splitTerms(arr[1]); + fullname.addAll(surname); + fullname.addAll(name); + } + } else { + fullname = splitTerms(s); + + int lastInitialPosition = fullname.size(); + boolean hasSurnameInUpperCase = false; + + for (int i = 0; i < fullname.size(); i++) { + final String term = fullname.get(i); + if (term.length() == 1) { + lastInitialPosition = i; + } else if (term.equals(term.toUpperCase())) { + hasSurnameInUpperCase = true; + } + } + + if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini + name = fullname.subList(0, lastInitialPosition + 1); + surname = fullname.subList(lastInitialPosition + 1, fullname.size()); + } else if (hasSurnameInUpperCase) { // Case: Michele ARTINI + for (final String term : fullname) { + if (term.length() > 1 && term.equals(term.toUpperCase())) { + surname.add(term); + } else { + name.add(term); + } + } + } + } + } + + private List splitTerms(final String s) { + if (particles == null) { + particles = loadFromClasspath("/eu/dnetlib/dhp/migration/pace/name_particles.txt"); + } + + final List list = Lists.newArrayList(); + for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) { + if (!particles.contains(part.toLowerCase())) { + list.add(part); + } + } + return list; + } + + public List getName() { + return name; + } + + public String getNameString() { + return Joiner.on(" ").join(getName()); + } + + public List getSurname() { + return surname; + } + + public List getFullname() { + return fullname; + } + + public String getOriginal() { + return original; + } + + public String hash() { + return Hashing.murmur3_128().hashString(getNormalisedFullname(), Charset.forName(UTF8)).toString(); + } + + public String getNormalisedFirstName() { + return Joiner.on(" ").join(getCapitalFirstnames()); + } + + public String getNormalisedSurname() { + return Joiner.on(" ").join(getCapitalSurname()); + } + + public String getSurnameString() { + return Joiner.on(" ").join(getSurname()); + } + + public String getNormalisedFullname() { + return isAccurate() ? getNormalisedSurname() + ", " + getNormalisedFirstName() : Joiner.on(" ").join(fullname); + } + + public List getCapitalFirstnames() { + return Lists.newArrayList(Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize)); + } + + public List getCapitalSurname() { + return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize)); + } + + public List getNameWithAbbreviations() { + return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations)); + } + + public boolean isAccurate() { + return name != null && surname != null && !name.isEmpty() && !surname.isEmpty(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json new file mode 100644 index 000000000..f179ee0f8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the HDFS source path which contains the sequential file", + "paramRequired": true + }, + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "g", + "paramLongName": "graphRawPath", + "paramDescription": "the path of the graph Raw in hdfs", + "paramRequired": true + }, + { + "paramName": "e", + "paramLongName": "entity", + "paramDescription": "The entity to extract", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json new file mode 100644 index 000000000..5e9f378f5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json @@ -0,0 +1,38 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "hdfsUser", + "paramDescription": "the user wich create the hdfs seq file", + "paramRequired": true + }, + { + "paramName": "dburl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "dbuser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "dbpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json new file mode 100644 index 000000000..5738daa76 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json @@ -0,0 +1,68 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "hdfsUser", + "paramDescription": "the user wich create the hdfs seq file", + "paramRequired": true + }, + { + "paramName": "mongourl", + "paramLongName": "mongoBaseUrl", + "paramDescription": "mongoDB url, example: mongodb://[username:password@]host[:port]", + "paramRequired": true + }, + { + "paramName": "db", + "paramLongName": "mongoDb", + "paramDescription": "mongo database", + "paramRequired": true + }, + { + "paramName": "f", + "paramLongName": "mdFormat", + "paramDescription": "metadata format", + "paramRequired": true + }, + { + "paramName": "l", + "paramLongName": "mdLayout", + "paramDescription": "metadata layout", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "mdInterpretation", + "paramDescription": "metadata interpretation", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/config-default.xml new file mode 100644 index 000000000..51e48d8f7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/config-default.xml @@ -0,0 +1,22 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hdfsUser + dnet + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml new file mode 100644 index 000000000..309a6d90f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml @@ -0,0 +1,282 @@ + + + + workingPath + the base path to store hdfs file + + + graphRawPath + the graph Raw base path + + + + postgresURL + the postgres URL to access to the database + + + postgresUser + the user postgres + + + postgresPassword + the password postgres + + + mongourl + mongoDB url, example: mongodb://[username:password@]host[:port] + + + mongoDb + mongo database + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.migration.MigrateDbEntitiesApplication + -p${workingPath}/db_entities + -n${nameNode} + -u${hdfsUser} + -dburl${postgresURL} + -dbuser${postgresUser} + -dbpasswd${postgresPassword} + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication + -p${workingPath}/odf_entities + -n${nameNode} + -u${hdfsUser} + -mongourl${mongourl} + -db${mongoDb} + -fODF + -lstore + -icleaned + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication + -p${workingPath}/oaf_entities + -n${nameNode} + -u${hdfsUser} + -mongourl${mongourl} + -db${mongoDb} + -fOAF + -lstore + -icleaned + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: publication + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/publication + -epublication + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: dataset + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/dataset + -edataset + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: software + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/software + -esoftware + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: otherresearchproduct + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/otherresearchproduct + -eotherresearchproduct + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: datasource + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/datasource + -edatasource + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: organization + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/organization + -eorganization + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: project + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/project + -eproject + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + ExtractEntities: relation + eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob + dhp-aggregation-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse" + -mt yarn-cluster + --sourcePath${workingPath} + -g${graphRawPath}/relation + -erelation + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/pace/name_particles.txt b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/pace/name_particles.txt new file mode 100644 index 000000000..dae37c9dc --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/pace/name_particles.txt @@ -0,0 +1,7 @@ +van +der +de +dell +sig +mr +mrs diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasourceOrganization.sql new file mode 100644 index 000000000..745f83971 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasourceOrganization.sql @@ -0,0 +1,17 @@ +SELECT + dor.datasource AS datasource, + dor.organization AS organization, + NULL AS startdate, + NULL AS enddate, + false AS inferred, + false AS deletedbyinference, + 0.9 AS trust, + NULL AS inferenceprovenance, + dc.id AS collectedfromid, + dc.officialname AS collectedfromname, + 'providedBy@@@provided by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS semantics, + d.provenanceaction || '@@@' || d.provenanceaction || '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction + +FROM dsm_datasource_organization dor + LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) + LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql new file mode 100644 index 000000000..8c587f34e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql @@ -0,0 +1,147 @@ +SELECT + d.id AS datasourceid, + d.id || array_agg(distinct di.pid) AS identities, + d.officialname AS officialname, + d.englishname AS englishname, + d.contactemail AS contactemail, + CASE + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire-cris_1.1']) + THEN + 'openaire-cris_1.1@@@OpenAIRE CRIS v1.1@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) + THEN + 'driver-openaire2.0@@@OpenAIRE 2.0+ (DRIVER OA, EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['driver']) + THEN + 'driver@@@OpenAIRE Basic (DRIVER OA)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0']) + THEN + 'openaire2.0@@@OpenAIRE 2.0 (EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire3.0']) + THEN + 'openaire3.0@@@OpenAIRE 3.0 (OA, funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0_data']) + THEN + 'openaire2.0_data@@@OpenAIRE Data (funded, referenced datasets)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['native']) + THEN + 'native@@@proprietary@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['hostedBy']) + THEN + 'hostedBy@@@collected from a compatible aggregator@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['notCompatible']) + THEN + 'notCompatible@@@under validation@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + ELSE + 'UNKNOWN@@@not available@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + END AS openairecompatibility, + d.websiteurl AS websiteurl, + d.logourl AS logourl, + array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END) AS accessinfopackage, + d.latitude AS latitude, + d.longitude AS longitude, + d.namespaceprefix AS namespaceprefix, + NULL AS odnumberofitems, + NULL AS odnumberofitemsdate, + + (SELECT array_agg(s|| '###keywords@@@keywords@@@dnet:subject_classification_typologies@@@dnet:subject_classification_typologies') + FROM UNNEST( + ARRAY( + SELECT trim(s) + FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, + + d.description AS description, + NULL AS odpolicies, + ARRAY(SELECT trim(s) + FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, + ARRAY(SELECT trim(s) + FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + false AS inferred, + false AS deletedbyinference, + 0.9 AS trust, + NULL AS inferenceprovenance, + d.dateofcollection AS dateofcollection, + d.dateofvalidation AS dateofvalidation, + -- re3data fields + d.releasestartdate AS releasestartdate, + d.releaseenddate AS releaseenddate, + d.missionstatementurl AS missionstatementurl, + d.dataprovider AS dataprovider, + d.serviceprovider AS serviceprovider, + d.databaseaccesstype AS databaseaccesstype, + d.datauploadtype AS datauploadtype, + d.databaseaccessrestriction AS databaseaccessrestriction, + d.datauploadrestriction AS datauploadrestriction, + d.versioning AS versioning, + d.citationguidelineurl AS citationguidelineurl, + d.qualitymanagementkind AS qualitymanagementkind, + d.pidsystems AS pidsystems, + d.certificates AS certificates, + ARRAY[]::text[] AS policies, + dc.id AS collectedfromid, + dc.officialname AS collectedfromname, + d.typology || '@@@' || CASE + WHEN (d.typology = 'crissystem') THEN 'CRIS System' + WHEN (d.typology = 'datarepository::unknown') THEN 'Data Repository' + WHEN (d.typology = 'aggregator::datarepository') THEN 'Data Repository Aggregator' + WHEN (d.typology = 'infospace') THEN 'Information Space' + WHEN (d.typology = 'pubsrepository::institutional') THEN 'Institutional Repository' + WHEN (d.typology = 'aggregator::pubsrepository::institutional') THEN 'Institutional Repository Aggregator' + WHEN (d.typology = 'pubsrepository::journal') THEN 'Journal' + WHEN (d.typology = 'aggregator::pubsrepository::journals') THEN 'Journal Aggregator/Publisher' + WHEN (d.typology = 'pubsrepository::mock') THEN 'Other' + WHEN (d.typology = 'pubscatalogue::unknown') THEN 'Publication Catalogue' + WHEN (d.typology = 'pubsrepository::unknown') THEN 'Publication Repository' + WHEN (d.typology = 'aggregator::pubsrepository::unknown') THEN 'Publication Repository Aggregator' + WHEN (d.typology = 'entityregistry') THEN 'Registry' + WHEN (d.typology = 'scholarcomminfra') THEN 'Scholarly Comm. Infrastructure' + WHEN (d.typology = 'pubsrepository::thematic') THEN 'Thematic Repository' + WHEN (d.typology = 'websource') THEN 'Web Source' + WHEN (d.typology = 'entityregistry::projects') THEN 'Funder database' + WHEN (d.typology = 'entityregistry::repositories') THEN 'Registry of repositories' + WHEN (d.typology = 'softwarerepository') THEN 'Software Repository' + WHEN (d.typology = 'aggregator::softwarerepository') THEN 'Software Repository Aggregator' + WHEN (d.typology = 'orprepository') THEN 'Repository' + ELSE 'Other' + END || '@@@dnet:datasource_typologies@@@dnet:datasource_typologies' AS datasourcetype, + 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + CONCAT(d.issn, '@@@', d.eissn, '@@@', d.lissn) AS journal + +FROM dsm_datasources d + +LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id) +LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource) +LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource) + +GROUP BY + d.id, + d.officialname, + d.englishname, + d.websiteurl, + d.logourl, + d.contactemail, + d.namespaceprefix, + d.description, + d.latitude, + d.longitude, + d.dateofcollection, + d.dateofvalidation, + d.releasestartdate, + d.releaseenddate, + d.missionstatementurl, + d.dataprovider, + d.serviceprovider, + d.databaseaccesstype, + d.datauploadtype, + d.databaseaccessrestriction, + d.datauploadrestriction, + d.versioning, + d.citationguidelineurl, + d.qualitymanagementkind, + d.pidsystems, + d.certificates, + dc.id, + dc.officialname, + d.issn, + d.eissn, + d.lissn diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizations.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizations.sql new file mode 100644 index 000000000..682ca3596 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizations.sql @@ -0,0 +1,36 @@ +SELECT + o.id AS organizationid, + o.legalshortname AS legalshortname, + o.legalname AS legalname, + o.websiteurl AS websiteurl, + o.logourl AS logourl, + o.ec_legalbody AS eclegalbody, + o.ec_legalperson AS eclegalperson, + o.ec_nonprofit AS ecnonprofit, + o.ec_researchorganization AS ecresearchorganization, + o.ec_highereducation AS echighereducation, + o.ec_internationalorganizationeurinterests AS ecinternationalorganizationeurinterests, + o.ec_internationalorganization AS ecinternationalorganization, + o.ec_enterprise AS ecenterprise, + o.ec_smevalidated AS ecsmevalidated, + o.ec_nutscode AS ecnutscode, + o.dateofcollection AS dateofcollection, + o.lastupdate AS dateoftransformation, + false AS inferred, + false AS deletedbyinference, + o.trust AS trust, + '' AS inferenceprovenance, + d.id AS collectedfromid, + d.officialname AS collectedfromname, + + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + + ARRAY[]::text[] AS pid +FROM dsm_organizations o + LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizationsFromOpenOrgsDB.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizationsFromOpenOrgsDB.sql new file mode 100644 index 000000000..dc9550883 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizationsFromOpenOrgsDB.sql @@ -0,0 +1,53 @@ +SELECT + o.id AS organizationid, + coalesce((array_agg(a.acronym))[1], o.name) AS legalshortname, + o.name AS legalname, + array_agg(DISTINCT n.name) AS "alternativeNames", + (array_agg(u.url))[1] AS websiteurl, + o.modification_date AS dateoftransformation, + false AS inferred, + false AS deletedbyinference, + 0.95 AS trust, + '' AS inferenceprovenance, + 'openaire____::openorgs' AS collectedfromid, + 'OpenOrgs Database' AS collectedfromname, + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid +FROM organizations o + LEFT OUTER JOIN acronyms a ON (a.id = o.id) + LEFT OUTER JOIN urls u ON (u.id = o.id) + LEFT OUTER JOIN other_ids i ON (i.id = o.id) + LEFT OUTER JOIN other_names n ON (n.id = o.id) +GROUP BY + o.id, + o.name, + o.modification_date, + o.country + +UNION ALL + +SELECT + 'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS organizationid, + n.name AS legalshortname, + n.name AS legalname, + ARRAY[]::text[] AS "alternativeNames", + (array_agg(u.url))[1] AS websiteurl, + o.modification_date AS dateoftransformation, + false AS inferred, + false AS deletedbyinference, + 0.88 AS trust, + '' AS inferenceprovenance, + 'openaire____::openorgs' AS collectedfromid, + 'OpenOrgs Database' AS collectedfromname, + o.country || '@@@dnet:countries' AS country, + 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction, + array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid +FROM other_names n + LEFT OUTER JOIN organizations o ON (n.id = o.id) + LEFT OUTER JOIN urls u ON (u.id = o.id) + LEFT OUTER JOIN other_ids i ON (i.id = o.id) +GROUP BY + o.id, o.modification_date, o.country, n.name + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjectOrganization.sql new file mode 100644 index 000000000..4c06ca5b9 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjectOrganization.sql @@ -0,0 +1,19 @@ +SELECT + po.project AS project, + po.resporganization AS resporganization, + po.participantnumber AS participantnumber, + po.contribution AS contribution, + NULL AS startdate, + NULL AS enddate, + false AS inferred, + false AS deletedbyinference, + po.trust AS trust, + NULL AS inferenceprovenance, + dc.id AS collectedfromid, + dc.officialname AS collectedfromname, + po.semanticclass || '@@@' || po.semanticclass || '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics, + 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction + +FROM project_organization po + LEFT OUTER JOIN projects p ON (p.id = po.project) + LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql new file mode 100644 index 000000000..6cff18875 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql @@ -0,0 +1,90 @@ +SELECT + p.id AS projectid, + p.code AS code, + p.websiteurl AS websiteurl, + p.acronym AS acronym, + p.title AS title, + p.startdate AS startdate, + p.enddate AS enddate, + p.call_identifier AS callidentifier, + p.keywords AS keywords, + p.duration AS duration, + p.ec_sc39 AS ecsc39, + p.oa_mandate_for_publications AS oamandatepublications, + p.ec_article29_3 AS ecarticle29_3, + p.dateofcollection AS dateofcollection, + p.lastupdate AS dateoftransformation, + p.inferred AS inferred, + p.deletedbyinference AS deletedbyinference, + p.trust AS trust, + p.inferenceprovenance AS inferenceprovenance, + p.optional1 AS optional1, + p.optional2 AS optional2, + p.jsonextrainfo AS jsonextrainfo, + p.contactfullname AS contactfullname, + p.contactfax AS contactfax, + p.contactphone AS contactphone, + p.contactemail AS contactemail, + p.summary AS summary, + p.currency AS currency, + p.totalcost AS totalcost, + p.fundedamount AS fundedamount, + dc.id AS collectedfromid, + dc.officialname AS collectedfromname, + ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name AS contracttype, + pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction, + array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, + array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects, + array_agg(DISTINCT fp.path) AS fundingtree + FROM projects p + LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass) + LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme) + + LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) + LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) + + LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) + + LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) + LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) + + LEFT OUTER JOIN project_subject ps ON (ps.project = p.id) + LEFT OUTER JOIN subjects s ON (s.id = ps.subject) + + LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass) + LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme) + + LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass) + LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme) + + GROUP BY + p.id, + p.code, + p.websiteurl, + p.acronym, + p.title, + p.startdate, + p.enddate, + p.call_identifier, + p.keywords, + p.duration, + p.ec_sc39, + p.oa_mandate_for_publications, + p.ec_article29_3, + p.dateofcollection, + p.inferred, + p.deletedbyinference, + p.trust, + p.inferenceprovenance, + p.contactfullname, + p.contactfax, + p.contactphone, + p.contactemail, + p.summary, + p.currency, + p.totalcost, + p.fundedamount, + dc.id, + dc.officialname, + pac.code, pac.name, pas.code, pas.name, + ctc.code, ctc.name, cts.code, cts.name; \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/querySimilarityFromOpenOrgsDB.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/querySimilarityFromOpenOrgsDB.sql new file mode 100644 index 000000000..4407559c6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/querySimilarityFromOpenOrgsDB.sql @@ -0,0 +1,17 @@ +SELECT local_id AS id1, oa_original_id AS id2 FROM openaire_simrels WHERE reltype = 'is_similar' + +UNION ALL + +SELECT + o.id AS id1, + 'openorgsmesh'||substring(o.id, 13)||'-'||md5(a.acronym) AS id2 +FROM acronyms a + LEFT OUTER JOIN organizations o ON (a.id = o.id) + +UNION ALL + +SELECT + o.id AS id1, + 'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS id2 +FROM other_names n + LEFT OUTER JOIN organizations o ON (n.id = o.id) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties b/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties new file mode 100644 index 000000000..63cba917e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties @@ -0,0 +1,9 @@ +# Set root logger level to DEBUG and its only appender to A1. +log4j.rootLogger=INFO, A1 + +# A1 is set to be a ConsoleAppender. +log4j.appender.A1=org.apache.log4j.ConsoleAppender + +# A1 uses PatternLayout. +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n diff --git a/dhp-workflows/dhp-dedup/pom.xml b/dhp-workflows/dhp-dedup/pom.xml index 28ef6a453..0721af25d 100644 --- a/dhp-workflows/dhp-dedup/pom.xml +++ b/dhp-workflows/dhp-dedup/pom.xml @@ -1,14 +1,44 @@ - + dhp-workflows eu.dnetlib.dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT 4.0.0 dhp-dedup + + + + + net.alchim31.maven + scala-maven-plugin + 4.0.1 + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + + ${scala.version} + + + + + diff --git a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json index 4e8b66d1b..090c94c26 100644 --- a/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json +++ b/dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json @@ -1,3 +1,3 @@ -{"journal":{"name":"","issnPrinted":"","issnOnline":"","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":"","conferencedate":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"author":[{"fullname":"Nemkov, Pavel G.","name":"","surname":"","rank":1,"pid":[],"affiliation":[]},{"fullname":"Gayubo, Severiano F.","name":"","surname":"","rank":2,"pid":[{"value":"ORCID1","qualifier":{"classid":"orcid","classname":"orcid","schemeid":"dnet:pidType","schemename":"dnet:pidType"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"affiliation":[]},{"fullname":"Ciccio Pasticcio","name":"","surname":"","rank":2,"pid":[],"affiliation":[]}],"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"und","classname":"Undetermined","schemeid":"dent:languages","schemename":"dent:languages"},"country":[],"subject":[{"value":"Biodiversity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Taxonomy","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Animalia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Arthropoda","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Insecta","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Hymenoptera","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Crabronidae","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"title":[{"value":"A New Species Of Nysson Latreille (Hymenoptera: Crabronidae: Bembicinae) From Turkmenistan","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"relevantdate":[{"value":"2003-12-31","qualifier":{"classid":"dnet:date","classname":"dnet:date","schemeid":"dnet:date","schemename":"dnet:date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"description":[{"value":"Nemkov, Pavel G., Gayubo, Severiano F. (2003): A new species of Nysson Latreille (Hymenoptera: Crabronidae: Bembicinae) from Turkmenistan. 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+{"journal":{"name":"","issnPrinted":"","issnOnline":"","issnLinking":"","ep":"","iss":"","sp":"","vol":"","edition":"","conferenceplace":"","conferencedate":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"author":[],"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"und","classname":"Undetermined","schemeid":"dent:languages","schemename":"dent:languages"},"country":[],"subject":[{"value":"Biodiversity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Taxonomy","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Animalia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Arthropoda","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Insecta","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Hymenoptera","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},{"value":"Crabronidae","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject","schemename":"dnet:subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"title":[{"value":"A New Species Of Nysson Latreille (Hymenoptera: Crabronidae: Bembicinae) From Turkmenistan","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"relevantdate":[{"value":"2003-12-31","qualifier":{"classid":"dnet:date","classname":"dnet:date","schemeid":"dnet:date","schemename":"dnet:date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"description":[{"value":"Nemkov, Pavel G., Gayubo, Severiano F. (2003): A new species of Nysson Latreille (Hymenoptera: Crabronidae: Bembicinae) from Turkmenistan. Zootaxa 144: 1-4, DOI: 10.5281/zenodo.156314","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"dateofacceptance":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"publisher":{"value":"Zenodo","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"embargoenddate":{"value":"","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}},"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":{"classid":"","classname":"","schemeid":"","schemename":""},"coverage":[],"context":[],"id":"50|scholexplore::ceb3a5d32107897a0df1178211e3e9ca","originalId":[],"collectedfrom":[{"key":"10|openaire____::e034d6a11054f5ade9221ebac484e864","value":"scholExplorer","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"pid":[{"value":"10.5281/zenodo.156314","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}}}],"extraInfo":[],"dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":true,"inferenceprovenance":"dedup-similarity-result-levenstein","provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":0} diff --git a/dhp-workflows/dhp-distcp/pom.xml b/dhp-workflows/dhp-distcp/pom.xml index 3b2f3176b..c3f09b42c 100644 --- a/dhp-workflows/dhp-distcp/pom.xml +++ b/dhp-workflows/dhp-distcp/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 9186fa829..802c3ff21 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -3,7 +3,7 @@ dhp-workflows eu.dnetlib.dhp - 1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT 4.0.0 diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/GraphMappingUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/GraphMappingUtils.java index ab19ff2b5..7c0967b2e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/GraphMappingUtils.java @@ -1,23 +1,31 @@ package eu.dnetlib.dhp.graph; -import com.google.common.collect.Maps; -import eu.dnetlib.dhp.schema.oaf.*; - import java.util.Map; +import com.google.common.collect.Maps; + +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.Software; + public class GraphMappingUtils { - public final static Map types = Maps.newHashMap(); + public final static Map types = Maps.newHashMap(); - static { - types.put("datasource", Datasource.class); - types.put("organization", Organization.class); - types.put("project", Project.class); - types.put("dataset", Dataset.class); - types.put("otherresearchproduct", OtherResearchProduct.class); - types.put("software", Software.class); - types.put("publication", Publication.class); - types.put("relation", Relation.class); - } + static { + types.put("datasource", Datasource.class); + types.put("organization", Organization.class); + types.put("project", Project.class); + types.put("dataset", Dataset.class); + types.put("otherresearchproduct", OtherResearchProduct.class); + types.put("software", Software.class); + types.put("publication", Publication.class); + types.put("relation", Relation.class); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java index a6a4e9291..c5223c1f6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/graph/SparkGraphImporterJob.java @@ -4,12 +4,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; -import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import scala.Tuple2; public class SparkGraphImporterJob { @@ -33,17 +31,12 @@ public class SparkGraphImporterJob { // Read the input file and convert it into RDD of serializable object GraphMappingUtils.types.forEach((name, clazz) -> { - final JavaRDD> inputRDD = sc.sequenceFile(inputPath + "/" + name, Text.class, Text.class) - .map(item -> new Tuple2<>(item._1.toString(), item._2.toString())); - - spark.createDataset(inputRDD - .filter(s -> s._1().equals(clazz.getName())) - .map(Tuple2::_2) - .map(s -> new ObjectMapper().readValue(s, clazz)) + spark.createDataset(sc.sequenceFile(inputPath + "/" + name, Text.class, Text.class) + .map(s -> new ObjectMapper().readValue(s._2().toString(), clazz)) .rdd(), Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .saveAsTable(hiveDbName + "." + name); + .write() + .mode(SaveMode.Overwrite) + .saveAsTable(hiveDbName + "." + name); }); } diff --git a/dhp-workflows/dhp-graph-provision/job-override.properties b/dhp-workflows/dhp-graph-provision/job-override.properties new file mode 100644 index 000000000..b5ab07982 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/job-override.properties @@ -0,0 +1,10 @@ +sparkDriverMemory=8G +sparkExecutorMemory=8G +#isLookupUrl=http://services.openaire.eu:8280/is/services/isLookUp +isLookupUrl=http://beta.services.openaire.eu:8280/is/services/isLookUp?wsdl +sourcePath=/tmp/db_openaireplus_services.export_dhp.2020.02.03 +outputPath=/tmp/openaire_provision +format=TMF +batchSize=2000 +sparkExecutorCoresForIndexing=64 +reuseRecords=true \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml new file mode 100644 index 000000000..f74c9b666 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -0,0 +1,92 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.1.6-SNAPSHOT + + 4.0.0 + + dhp-graph-provision + + + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + com.jayway.jsonpath + json-path + + + dom4j + dom4j + + + jaxen + jaxen + + + com.mycila.xmltool + xmltool + + + org.antlr + stringtemplate + + + org.apache.solr + solr-solrj + + + com.lucidworks.spark + spark-solr + + + + org.apache.httpcomponents + httpclient + + + org.apache.httpcomponents + httpmime + + + + org.noggit + noggit + + + org.apache.zookeeper + zookeeper + + + + org.apache.cxf + cxf-rt-transports-http + + + eu.dnetlib + cnr-rmi-api + + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/GraphJoiner.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/GraphJoiner.java new file mode 100644 index 000000000..062c8886b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/GraphJoiner.java @@ -0,0 +1,257 @@ +package eu.dnetlib.dhp.graph; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Iterables; +import com.google.common.collect.Lists; +import com.jayway.jsonpath.DocumentContext; +import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.graph.model.*; +import eu.dnetlib.dhp.graph.utils.ContextMapper; +import eu.dnetlib.dhp.graph.utils.GraphMappingUtils; +import eu.dnetlib.dhp.graph.utils.XmlRecordFactory; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.PairFunction; +import org.apache.spark.sql.SparkSession; +import scala.Tuple2; + +import java.io.IOException; +import java.io.Serializable; +import java.util.HashSet; +import java.util.List; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.graph.utils.GraphMappingUtils.asRelatedEntity; + +/** + * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. + * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, + * and all the possible relationships (similarity links produced by the Dedup process are excluded). + * + * The operation is implemented creating the union between the entity types (E), joined by the relationships (R), and again + * by E, finally grouped by E.id; + * + * Different manipulations of the E and R sets are introduced to reduce the complexity of the operation + * 1) treat the object payload as string, extracting only the necessary information beforehand using json path, + * it seems that deserializing it with jackson's object mapper has higher memory footprint. + * + * 2) only consider rels that are not virtually deleted ($.dataInfo.deletedbyinference == false) + * 3) we only need a subset of fields from the related entities, so we introduce a distinction between E_source = S + * and E_target = T. Objects in T are heavily pruned by all the unnecessary information + * + * 4) perform the join as (((T join R) union S) groupby S.id) yield S -> [ ] + */ +public class GraphJoiner implements Serializable { + + public static final int MAX_RELS = 100; + + public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd"; + + private SparkSession spark; + + private ContextMapper contextMapper; + + private String inputPath; + + private String outPath; + + public GraphJoiner(SparkSession spark, ContextMapper contextMapper, String inputPath, String outPath) { + this.spark = spark; + this.contextMapper = contextMapper; + this.inputPath = inputPath; + this.outPath = outPath; + } + + public GraphJoiner adjacencyLists() { + final JavaSparkContext sc = new JavaSparkContext(getSpark().sparkContext()); + + // read each entity + JavaPairRDD datasource = readPathEntity(sc, getInputPath(), "datasource"); + JavaPairRDD organization = readPathEntity(sc, getInputPath(), "organization"); + JavaPairRDD project = readPathEntity(sc, getInputPath(), "project"); + JavaPairRDD dataset = readPathEntity(sc, getInputPath(), "dataset"); + JavaPairRDD otherresearchproduct = readPathEntity(sc, getInputPath(), "otherresearchproduct"); + JavaPairRDD software = readPathEntity(sc, getInputPath(), "software"); + JavaPairRDD publication = readPathEntity(sc, getInputPath(), "publication"); + + // create the union between all the entities + final String entitiesPath = getOutPath() + "/entities"; + datasource + .union(organization) + .union(project) + .union(dataset) + .union(otherresearchproduct) + .union(software) + .union(publication) + .map(e -> new EntityRelEntity().setSource(e._2())) + .map(GraphMappingUtils::serialize) + .saveAsTextFile(entitiesPath, GzipCodec.class); + + JavaPairRDD entities = sc.textFile(entitiesPath) + .map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class)) + .mapToPair(t -> new Tuple2<>(t.getSource().getSourceId(), t)); + + // reads the relationships + final JavaPairRDD relation = readPathRelation(sc, getInputPath()) + .filter(r -> !r.getDeleted()) //only consider those that are not virtually deleted + .map(p -> new EntityRelEntity().setRelation(p)) + .mapToPair(p -> new Tuple2<>(p.getRelation().getSourceId(), p)) + .groupByKey() + .map(p -> Iterables.limit(p._2(), MAX_RELS)) + .flatMap(p -> p.iterator()) + .mapToPair(p -> new Tuple2<>(p.getRelation().getTargetId(), p)); + + //final String bySource = getOutPath() + "/1_join_by_target"; + JavaPairRDD bySource = relation + .join(entities + .filter(e -> !e._2().getSource().getDeleted()) + .mapToPair(e -> new Tuple2<>(e._1(), asRelatedEntity(e._2())))) + .map(s -> new EntityRelEntity() + .setRelation(s._2()._1().getRelation()) + .setTarget(s._2()._2().getSource())) + .mapToPair(t -> new Tuple2<>(t.getRelation().getSourceId(), t)); + + final XmlRecordFactory recordFactory = new XmlRecordFactory(contextMapper, false, schemaLocation, new HashSet<>()); + entities + .union(bySource) + .groupByKey() // by source id + .map(l -> toJoinedEntity(l)) + .mapToPair(je -> new Tuple2<>( + new Text(je.getEntity().getId()), + new Text(recordFactory.build(je)))) + .saveAsHadoopFile(getOutPath() + "/xml", Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + return this; + } + + public GraphJoiner asXML() { + final JavaSparkContext sc = new JavaSparkContext(getSpark().sparkContext()); + final XmlRecordFactory recordFactory = new XmlRecordFactory(contextMapper, true, "", new HashSet<>()); + final ObjectMapper mapper = new ObjectMapper(); + + final String joinedEntitiesPath = getOutPath() + "/1_joined_entities"; + sc.textFile(joinedEntitiesPath) + .map(s -> mapper.readValue(s, JoinedEntity.class)) + .mapToPair(je -> new Tuple2<>(new Text(je.getEntity().getId()), new Text(recordFactory.build(je)))) + .saveAsHadoopFile(getOutPath() + "/2_xml", Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + return this; + } + + public SparkSession getSpark() { + return spark; + } + + public String getInputPath() { + return inputPath; + } + + public String getOutPath() { + return outPath; + } + + // HELPERS + + private OafEntity parseOaf(final String json, final String type) { + final ObjectMapper o = new ObjectMapper(); + try { + switch (GraphMappingUtils.EntityType.valueOf(type)) { + case publication: + return o.readValue(json, Publication.class); + case dataset: + return o.readValue(json, Dataset.class); + case otherresearchproduct: + return o.readValue(json, OtherResearchProduct.class); + case software: + return o.readValue(json, Software.class); + case datasource: + return o.readValue(json, Datasource.class); + case organization: + return o.readValue(json, Organization.class); + case project: + return o.readValue(json, Project.class); + default: + throw new IllegalArgumentException("invalid type: " + type); + } + } catch (IOException e) { + throw new IllegalArgumentException(e); + } + } + + private JoinedEntity toJoinedEntity(Tuple2> p) { + final ObjectMapper o = new ObjectMapper(); + final JoinedEntity j = new JoinedEntity(); + final Links links2 = new Links(); + for(EntityRelEntity rel : p._2()) { + if (rel.hasMainEntity() & j.getEntity() == null) { + j.setType(rel.getSource().getType()); + j.setEntity(parseOaf(rel.getSource().getOaf(), rel.getSource().getType())); + } + if (rel.hasRelatedEntity()) { + try { + links2.add( + new eu.dnetlib.dhp.graph.model.Tuple2() + .setRelation(o.readValue(rel.getRelation().getOaf(), Relation.class)) + .setRelatedEntity(o.readValue(rel.getTarget().getOaf(), RelatedEntity.class))); + } catch (IOException e) { + throw new IllegalArgumentException(e); + } + } + } + j.setLinks(links2); + if (j.getEntity() == null) { + throw new IllegalStateException("missing main entity on '" + p._1() + "'"); + } + return j; + } + + /** + * Reads a set of eu.dnetlib.dhp.schema.oaf.OafEntity objects from a sequence file , + * extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow + * @param sc + * @param inputPath + * @param type + * @return the JavaPairRDD indexed by entity identifier + */ + private JavaPairRDD readPathEntity(final JavaSparkContext sc, final String inputPath, final String type) { + return sc.sequenceFile(inputPath + "/" + type, Text.class, Text.class) + .mapToPair((PairFunction, String, TypedRow>) item -> { + final String s = item._2().toString(); + final DocumentContext json = JsonPath.parse(s); + final String id = json.read("$.id"); + return new Tuple2<>(id, new TypedRow() + .setSourceId(id) + .setDeleted(json.read("$.dataInfo.deletedbyinference")) + .setType(type) + .setOaf(s)); + }); + } + + /** + * Reads a set of eu.dnetlib.dhp.schema.oaf.Relation objects from a sequence file , + * extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow + * @param sc + * @param inputPath + * @return the JavaRDD containing all the relationships + */ + private JavaRDD readPathRelation(final JavaSparkContext sc, final String inputPath) { + return sc.sequenceFile(inputPath + "/relation", Text.class, Text.class) + .map(item -> { + final String s = item._2().toString(); + final DocumentContext json = JsonPath.parse(s); + return new TypedRow() + .setSourceId(json.read("$.source")) + .setTargetId(json.read("$.target")) + .setDeleted(json.read("$.dataInfo.deletedbyinference")) + .setType("relation") + .setOaf(s); + }); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java new file mode 100644 index 000000000..2775d93b4 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java @@ -0,0 +1,188 @@ +package eu.dnetlib.dhp.graph; + +import com.lucidworks.spark.util.SolrSupport; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.graph.utils.ISLookupClientFactory; +import eu.dnetlib.dhp.graph.utils.StreamingInputDocumentFactory; +import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.io.Text; +import org.apache.solr.common.SolrInputDocument; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.SparkSession; + +import javax.xml.transform.Transformer; +import javax.xml.transform.TransformerException; +import javax.xml.transform.stream.StreamResult; +import javax.xml.transform.stream.StreamSource; +import java.io.IOException; +import java.io.StringReader; +import java.io.StringWriter; +import java.text.SimpleDateFormat; +import java.util.Date; + +public class SparkXmlIndexingJob { + + private static final Log log = LogFactory.getLog(SparkXmlIndexingJob.class); + + private static final Integer DEFAULT_BATCH_SIZE = 1000; + + private static final String LAYOUT = "index"; + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkXmlIndexingJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_params_update_index.json"))); + parser.parseArgument(args); + + final String inputPath = parser.get("sourcePath"); + final String isLookupUrl = parser.get("isLookupUrl"); + final String format = parser.get("format"); + final Integer batchSize = parser.getObjectMap().containsKey("batchSize") ? Integer.valueOf(parser.get("batchSize")) : DEFAULT_BATCH_SIZE; + + final ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + final String fields = getLayoutSource(isLookup, format); + final String xslt = getLayoutTransformer(isLookup); + + final String dsId = getDsId(format, isLookup); + final String zkHost = getZkHost(isLookup); + final String version = getRecordDatestamp(); + + final String indexRecordXslt = getLayoutTransformer(format, fields, xslt); + + log.info("indexRecordTransformer: " + indexRecordXslt); + + final String master = parser.get("master"); + final SparkConf conf = new SparkConf() + .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + + try(SparkSession spark = getSession(conf, master)) { + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + RDD docs = sc.sequenceFile(inputPath, Text.class, Text.class) + .map(t -> t._2().toString()) + .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s)) + .map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s)) + .rdd(); + + SolrSupport.indexDocs(zkHost, format + "-" + LAYOUT + "-openaire", batchSize, docs); + } + } + + private static SparkSession getSession(SparkConf conf, String master) { + return SparkSession + .builder() + .config(conf) + .appName(SparkXmlRecordBuilderJob.class.getSimpleName()) + .master(master) + .getOrCreate(); + } + + private static String toIndexRecord(Transformer tr, final String record) { + final StreamResult res = new StreamResult(new StringWriter()); + try { + tr.transform(new StreamSource(new StringReader(record)), res); + return res.getWriter().toString(); + } catch (Throwable e) { + System.out.println("XPathException on record:\n" + record); + throw new IllegalArgumentException(e); + } + } + + /** + * Creates the XSLT responsible for building the index xml records. + * + * @param format Metadata format name (DMF|TMF) + * @param xslt xslt for building the index record transformer + * @param fields the list of fields + * @return the javax.xml.transform.Transformer + * @throws ISLookUpException could happen + * @throws IOException could happen + * @throws TransformerException could happen + */ + private static String getLayoutTransformer(String format, String fields, String xslt) throws TransformerException { + + final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt); + final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter()); + + layoutTransformer.setParameter("format", format); + layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt); + + return layoutToXsltXslt.getWriter().toString(); + } + + /** + * method return a solr-compatible string representation of a date, used to mark all records as indexed today + * @return the parsed date + */ + public static String getRecordDatestamp() { + return new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'").format(new Date()); + } + + /** + * Method retrieves from the information system the list of fields associated to the given MDFormat name + * + * @param isLookup the ISLookup service stub + * @param format the Metadata format name + * @return the string representation of the list of fields to be indexed + * + * @throws ISLookUpDocumentNotFoundException + * @throws ISLookUpException + */ + private static String getLayoutSource(final ISLookUpService isLookup, final String format) throws ISLookUpDocumentNotFoundException, ISLookUpException { + return doLookup(isLookup, String.format( + "collection('')//RESOURCE_PROFILE[.//RESOURCE_TYPE/@value = 'MDFormatDSResourceType' and .//NAME='%s']//LAYOUT[@name='%s']", format, LAYOUT)); + } + + /** + * Method retrieves from the information system the openaireLayoutToRecordStylesheet + * + * @param isLookup the ISLookup service stub + * @return the string representation of the XSLT contained in the transformation rule profile + * + * @throws ISLookUpDocumentNotFoundException + * @throws ISLookUpException + */ + private static String getLayoutTransformer(ISLookUpService isLookup) throws ISLookUpException { + return doLookup(isLookup, "collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType')" + + "//RESOURCE_PROFILE[./BODY/CONFIGURATION/SCRIPT/TITLE/text() = 'openaireLayoutToRecordStylesheet']//CODE/node()"); + } + + /** + * Method retrieves from the information system the IndexDS profile ID associated to the given MDFormat name + * @param format + * @param isLookup + * @return the IndexDS identifier + * @throws ISLookUpException + */ + private static String getDsId(String format, ISLookUpService isLookup) throws ISLookUpException { + return doLookup(isLookup, String.format("collection('/db/DRIVER/IndexDSResources/IndexDSResourceType')" + + "//RESOURCE_PROFILE[./BODY/CONFIGURATION/METADATA_FORMAT/text() = '%s']//RESOURCE_IDENTIFIER/@value/string()", format)); + } + + /** + * Method retrieves from the information system the zookeeper quorum of the Solr server + * @param isLookup + * @return the zookeeper quorum of the Solr server + * @throws ISLookUpException + */ + private static String getZkHost(ISLookUpService isLookup) throws ISLookUpException { + return doLookup(isLookup, "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()"); + } + + private static String doLookup(ISLookUpService isLookup, String xquery) throws ISLookUpException { + log.info(String.format("running xquery: %s", xquery)); + final String res = isLookup.getResourceProfileByQuery(xquery); + log.info(String.format("got response (100 chars): %s", StringUtils.left(res, 100) + " ...")); + return res; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlRecordBuilderJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlRecordBuilderJob.java new file mode 100644 index 000000000..0b2180f19 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlRecordBuilderJob.java @@ -0,0 +1,48 @@ +package eu.dnetlib.dhp.graph; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.graph.utils.ContextMapper; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; + +public class SparkXmlRecordBuilderJob { + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkXmlRecordBuilderJob.class.getResourceAsStream("/eu/dnetlib/dhp/graph/input_params_build_adjacency_lists.json"))); + parser.parseArgument(args); + + final String master = parser.get("master"); + final SparkConf conf = new SparkConf() + .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + + try(SparkSession spark = getSession(conf, master)) { + + final String inputPath = parser.get("sourcePath"); + final String outputPath = parser.get("outputPath"); + final String isLookupUrl = parser.get("isLookupUrl"); + + final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); + if (fs.exists(new Path(outputPath))) { + fs.delete(new Path(outputPath), true); + fs.mkdirs(new Path(outputPath)); + } + + new GraphJoiner(spark, ContextMapper.fromIS(isLookupUrl), inputPath, outputPath) + .adjacencyLists(); + } + } + + private static SparkSession getSession(SparkConf conf, String master) { + return SparkSession + .builder() + .config(conf) + .appName(SparkXmlRecordBuilderJob.class.getSimpleName()) + .master(master) + .getOrCreate(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/EntityRelEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/EntityRelEntity.java new file mode 100644 index 000000000..8c08337e2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/EntityRelEntity.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.graph.model; + +import java.io.Serializable; + +public class EntityRelEntity implements Serializable { + + private TypedRow source; + private TypedRow relation; + private TypedRow target; + + public EntityRelEntity() { + } + + public EntityRelEntity(TypedRow source) { + this.source = source; + } + + //helpers + public Boolean hasMainEntity() { + return getSource() != null & getRelation() == null & getTarget() == null; + } + + public Boolean hasRelatedEntity() { + return getSource() == null & getRelation() != null & getTarget() != null; + } + + + public TypedRow getSource() { + return source; + } + + public EntityRelEntity setSource(TypedRow source) { + this.source = source; + return this; + } + + public TypedRow getRelation() { + return relation; + } + + public EntityRelEntity setRelation(TypedRow relation) { + this.relation = relation; + return this; + } + + public TypedRow getTarget() { + return target; + } + + public EntityRelEntity setTarget(TypedRow target) { + this.target = target; + return this; + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/JoinedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/JoinedEntity.java new file mode 100644 index 000000000..f89273a0d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/JoinedEntity.java @@ -0,0 +1,41 @@ +package eu.dnetlib.dhp.graph.model; + +import eu.dnetlib.dhp.schema.oaf.OafEntity; + +import java.io.Serializable; + +public class JoinedEntity implements Serializable { + + private String type; + + private OafEntity entity; + + private Links links; + + public String getType() { + return type; + } + + public JoinedEntity setType(String type) { + this.type = type; + return this; + } + + public OafEntity getEntity() { + return entity; + } + + public JoinedEntity setEntity(OafEntity entity) { + this.entity = entity; + return this; + } + + public Links getLinks() { + return links; + } + + public JoinedEntity setLinks(Links links) { + this.links = links; + return this; + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Links.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Links.java new file mode 100644 index 000000000..96ad67b0c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Links.java @@ -0,0 +1,6 @@ +package eu.dnetlib.dhp.graph.model; + +import java.util.ArrayList; + +public class Links extends ArrayList { +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/RelatedEntity.java new file mode 100644 index 000000000..baeff1c6a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/RelatedEntity.java @@ -0,0 +1,257 @@ +package eu.dnetlib.dhp.graph.model; + +import eu.dnetlib.dhp.schema.oaf.Instance; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Qualifier; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.codehaus.jackson.map.ObjectMapper; + +import java.io.IOException; +import java.io.Serializable; +import java.util.List; + +public class RelatedEntity implements Serializable { + + private String id; + private String type; + + // common fields + private StructuredProperty title; + private String websiteurl; // datasource, organizations, projects + + // results + private String dateofacceptance; + private String publisher; + private List pid; + private String codeRepositoryUrl; + private Qualifier resulttype; + private List collectedfrom; + private List instances; + + // datasource + private String officialname; + private Qualifier datasourcetype; + private Qualifier datasourcetypeui; + private Qualifier openairecompatibility; + //private String aggregatortype; + + // organization + private String legalname; + private String legalshortname; + private Qualifier country; + + // project + private String projectTitle; + private String code; + private String acronym; + private Qualifier contracttype; + private List fundingtree; + + public String getId() { + return id; + } + + public RelatedEntity setId(String id) { + this.id = id; + return this; + } + + public StructuredProperty getTitle() { + return title; + } + + public RelatedEntity setTitle(StructuredProperty title) { + this.title = title; + return this; + } + + public String getDateofacceptance() { + return dateofacceptance; + } + + public RelatedEntity setDateofacceptance(String dateofacceptance) { + this.dateofacceptance = dateofacceptance; + return this; + } + + public String getPublisher() { + return publisher; + } + + public RelatedEntity setPublisher(String publisher) { + this.publisher = publisher; + return this; + } + + public List getPid() { + return pid; + } + + public RelatedEntity setPid(List pid) { + this.pid = pid; + return this; + } + + public String getCodeRepositoryUrl() { + return codeRepositoryUrl; + } + + public RelatedEntity setCodeRepositoryUrl(String codeRepositoryUrl) { + this.codeRepositoryUrl = codeRepositoryUrl; + return this; + } + + public Qualifier getResulttype() { + return resulttype; + } + + public RelatedEntity setResulttype(Qualifier resulttype) { + this.resulttype = resulttype; + return this; + } + + public List getCollectedfrom() { + return collectedfrom; + } + + public RelatedEntity setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + return this; + } + + public List getInstances() { + return instances; + } + + public RelatedEntity setInstances(List instances) { + this.instances = instances; + return this; + } + + public String getOfficialname() { + return officialname; + } + + public RelatedEntity setOfficialname(String officialname) { + this.officialname = officialname; + return this; + } + + public String getWebsiteurl() { + return websiteurl; + } + + public RelatedEntity setWebsiteurl(String websiteurl) { + this.websiteurl = websiteurl; + return this; + } + + public Qualifier getDatasourcetype() { + return datasourcetype; + } + + public RelatedEntity setDatasourcetype(Qualifier datasourcetype) { + this.datasourcetype = datasourcetype; + return this; + } + + public Qualifier getDatasourcetypeui() { + return datasourcetypeui; + } + + public RelatedEntity setDatasourcetypeui(Qualifier datasourcetypeui) { + this.datasourcetypeui = datasourcetypeui; + return this; + } + + public Qualifier getOpenairecompatibility() { + return openairecompatibility; + } + + public RelatedEntity setOpenairecompatibility(Qualifier openairecompatibility) { + this.openairecompatibility = openairecompatibility; + return this; + } + + public String getLegalname() { + return legalname; + } + + public RelatedEntity setLegalname(String legalname) { + this.legalname = legalname; + return this; + } + + public String getLegalshortname() { + return legalshortname; + } + + public RelatedEntity setLegalshortname(String legalshortname) { + this.legalshortname = legalshortname; + return this; + } + + public Qualifier getCountry() { + return country; + } + + public RelatedEntity setCountry(Qualifier country) { + this.country = country; + return this; + } + + public String getCode() { + return code; + } + + public RelatedEntity setCode(String code) { + this.code = code; + return this; + } + + public String getAcronym() { + return acronym; + } + + public RelatedEntity setAcronym(String acronym) { + this.acronym = acronym; + return this; + } + + public Qualifier getContracttype() { + return contracttype; + } + + public RelatedEntity setContracttype(Qualifier contracttype) { + this.contracttype = contracttype; + return this; + } + + public List getFundingtree() { + return fundingtree; + } + + public RelatedEntity setFundingtree(List fundingtree) { + this.fundingtree = fundingtree; + return this; + } + + public String getProjectTitle() { + return projectTitle; + } + + public RelatedEntity setProjectTitle(String projectTitle) { + this.projectTitle = projectTitle; + return this; + } + + public String getType() { + return type; + } + + public RelatedEntity setType(String type) { + this.type = type; + return this; + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Tuple2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Tuple2.java new file mode 100644 index 000000000..ab965808b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/Tuple2.java @@ -0,0 +1,28 @@ +package eu.dnetlib.dhp.graph.model; + +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class Tuple2 { + + private Relation relation; + + private RelatedEntity relatedEntity; + + public Relation getRelation() { + return relation; + } + + public Tuple2 setRelation(Relation relation) { + this.relation = relation; + return this; + } + + public RelatedEntity getRelatedEntity() { + return relatedEntity; + } + + public Tuple2 setRelatedEntity(RelatedEntity relatedEntity) { + this.relatedEntity = relatedEntity; + return this; + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/TypedRow.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/TypedRow.java new file mode 100644 index 000000000..3651e28c9 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/model/TypedRow.java @@ -0,0 +1,61 @@ +package eu.dnetlib.dhp.graph.model; + +import java.io.Serializable; + +public class TypedRow implements Serializable { + + private String sourceId; + + private String targetId; + + private Boolean deleted; + + private String type; + + private String oaf; + + public String getSourceId() { + return sourceId; + } + + public TypedRow setSourceId(String sourceId) { + this.sourceId = sourceId; + return this; + } + + public String getTargetId() { + return targetId; + } + + public TypedRow setTargetId(String targetId) { + this.targetId = targetId; + return this; + } + + public Boolean getDeleted() { + return deleted; + } + + public TypedRow setDeleted(Boolean deleted) { + this.deleted = deleted; + return this; + } + + public String getType() { + return type; + } + + public TypedRow setType(String type) { + this.type = type; + return this; + } + + public String getOaf() { + return oaf; + } + + public TypedRow setOaf(String oaf) { + this.oaf = oaf; + return this; + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextDef.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextDef.java new file mode 100644 index 000000000..05d9456f6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextDef.java @@ -0,0 +1,51 @@ +package eu.dnetlib.dhp.graph.utils; + +import java.io.Serializable; + +public class ContextDef implements Serializable { + + private String id; + private String label; + private String name; + private String type; + + public ContextDef(final String id, final String label, final String name, final String type) { + super(); + this.setId(id); + this.setLabel(label); + this.setName(name); + this.setType(type); + } + + public String getLabel() { + return label; + } + + public void setLabel(final String label) { + this.label = label; + } + + public String getId() { + return id; + } + + public void setId(final String id) { + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(final String name) { + this.name = name; + } + + public String getType() { + return type; + } + + public void setType(final String type) { + this.type = type; + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java new file mode 100644 index 000000000..0c3a481d0 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java @@ -0,0 +1,45 @@ +package eu.dnetlib.dhp.graph.utils; + +import com.google.common.base.Joiner; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Node; +import org.dom4j.io.SAXReader; + +import java.io.Serializable; +import java.io.StringReader; +import java.util.HashMap; + +public class ContextMapper extends HashMap implements Serializable { + + private static final long serialVersionUID = 2159682308502487305L; + + private final static String XQUERY = "for $x in //RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ContextDSResourceType']//*[name()='context' or name()='category' or name()='concept'] return "; + + public static ContextMapper fromIS(final String isLookupUrl) throws DocumentException, ISLookUpException { + ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl); + StringBuilder sb = new StringBuilder(""); + Joiner.on("").appendTo(sb, isLookUp.quickSearchProfile(XQUERY)); + sb.append(""); + return fromXml(sb.toString()); + } + + public static ContextMapper fromXml(final String xml) throws DocumentException { + final ContextMapper contextMapper = new ContextMapper(); + + final Document doc = new SAXReader().read(new StringReader(xml)); + for (Object o : doc.selectNodes("//entry")) { + Node node = (Node) o; + String id = node.valueOf("./@id"); + String label = node.valueOf("./@label"); + String name = node.valueOf("./@name"); + String type = node.valueOf("./@type") + ""; + + contextMapper.put(id, new ContextDef(id, label, name, type)); + } + return contextMapper; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/GraphMappingUtils.java new file mode 100644 index 000000000..0921fe105 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/GraphMappingUtils.java @@ -0,0 +1,254 @@ +package eu.dnetlib.dhp.graph.utils; + +import com.fasterxml.jackson.annotation.JsonInclude; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.base.Predicate; +import com.google.common.collect.BiMap; +import com.google.common.collect.HashBiMap; +import com.google.common.collect.Maps; +import com.google.common.collect.Sets; +import com.jayway.jsonpath.DocumentContext; +import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.graph.model.EntityRelEntity; +import eu.dnetlib.dhp.graph.model.RelatedEntity; +import eu.dnetlib.dhp.graph.model.TypedRow; +import eu.dnetlib.dhp.schema.oaf.*; +import net.minidev.json.JSONArray; +import org.apache.commons.lang3.StringUtils; + +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +import static org.apache.commons.lang3.StringUtils.*; + +public class GraphMappingUtils { + + public enum EntityType { + publication, dataset, otherresearchproduct, software, datasource, organization, project + } + + public enum MainEntityType { + result, datasource, organization, project + } + + public static Set authorPidTypes = Sets.newHashSet("orcid", "magidentifier"); + + public static Set instanceFieldFilter = Sets.newHashSet("instancetype", "hostedby", "license", "accessright", "collectedfrom", "dateofacceptance", "distributionlocation"); + + private static BiMap relClassMapping = HashBiMap.create(); + + static { + relClassMapping.put("isAuthorInstitutionOf", "hasAuthorInstitution"); + relClassMapping.put("isMergedIn", "merges"); + relClassMapping.put("isProducedBy", "produces"); + relClassMapping.put("hasParticipant", "isParticipant"); + relClassMapping.put("isProvidedBy", "provides"); + relClassMapping.put("isRelatedTo", "isRelatedTo"); + relClassMapping.put("isAmongTopNSimilarDocuments", "hasAmongTopNSimilarDocuments"); + relClassMapping.put("isRelatedTo", "isRelatedTo"); + relClassMapping.put("isSupplementTo", "isSupplementedBy"); + } + + public static String getInverseRelClass(final String relClass) { + String res = relClassMapping.get(relClass); + if (isNotBlank(res)) { + return res; + } + res = relClassMapping.inverse().get(relClass); + + if (isNotBlank(res)) { + return res; + } + + throw new IllegalArgumentException("unable to find an inverse relationship class for term: " + relClass); + } + + private static final String schemeTemplate = "dnet:%s_%s_relations"; + + private static Map entityMapping = Maps.newHashMap(); + + static { + entityMapping.put(EntityType.publication, MainEntityType.result); + entityMapping.put(EntityType.dataset, MainEntityType.result); + entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); + entityMapping.put(EntityType.software, MainEntityType.result); + entityMapping.put(EntityType.datasource, MainEntityType.datasource); + entityMapping.put(EntityType.organization, MainEntityType.organization); + entityMapping.put(EntityType.project, MainEntityType.project); + } + + public static String getScheme(final String sourceType, final String targetType) { + return String.format(schemeTemplate, + entityMapping.get(EntityType.valueOf(sourceType)).name(), + entityMapping.get(EntityType.valueOf(targetType)).name()); + } + + public static String getMainType(final String type) { + return entityMapping.get(EntityType.valueOf(type)).name(); + } + + public static boolean isResult(String type) { + return MainEntityType.result.name().equals(getMainType(type)); + } + + public static Predicate instanceFilter = s -> instanceFieldFilter.contains(s); + + public static EntityRelEntity asRelatedEntity(EntityRelEntity e) { + + final DocumentContext j = JsonPath.parse(e.getSource().getOaf()); + final RelatedEntity re = new RelatedEntity().setId(j.read("$.id")).setType(e.getSource().getType()); + + switch (EntityType.valueOf(e.getSource().getType())) { + case publication: + case dataset: + case otherresearchproduct: + case software: + mapTitle(j, re); + re.setDateofacceptance(j.read("$.dateofacceptance.value")); + re.setPublisher(j.read("$.publisher.value")); + + JSONArray pids = j.read("$.pid"); + re.setPid(pids.stream() + .map(p -> asStructuredProperty((LinkedHashMap) p)) + .collect(Collectors.toList())); + + re.setResulttype(asQualifier(j.read("$.resulttype"))); + + JSONArray collfrom = j.read("$.collectedfrom"); + re.setCollectedfrom(collfrom.stream() + .map(c -> asKV((LinkedHashMap) c)) + .collect(Collectors.toList())); + + // will throw exception when the instance is not found + JSONArray instances = j.read("$.instance"); + re.setInstances(instances.stream() + .map(i -> { + final LinkedHashMap p = (LinkedHashMap) i; + final Field license = new Field(); + license.setValue((String) ((LinkedHashMap) p.get("license")).get("value")); + final Instance instance = new Instance(); + instance.setLicense(license); + instance.setAccessright(asQualifier((LinkedHashMap) p.get("accessright"))); + instance.setInstancetype(asQualifier((LinkedHashMap) p.get("instancetype"))); + instance.setHostedby(asKV((LinkedHashMap) p.get("hostedby"))); + //TODO mapping of distributionlocation + instance.setCollectedfrom(asKV((LinkedHashMap) p.get("collectedfrom"))); + + Field dateofacceptance = new Field(); + dateofacceptance.setValue((String) ((LinkedHashMap) p.get("dateofacceptance")).get("value")); + instance.setDateofacceptance(dateofacceptance); + return instance; + }).collect(Collectors.toList())); + + //TODO still to be mapped + //re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); + + break; + case datasource: + re.setOfficialname(j.read("$.officialname.value")); + re.setWebsiteurl(j.read("$.websiteurl.value")); + re.setDatasourcetype(asQualifier(j.read("$.datasourcetype"))); + re.setOpenairecompatibility(asQualifier(j.read("$.openairecompatibility"))); + + break; + case organization: + re.setLegalname(j.read("$.legalname.value")); + re.setLegalshortname(j.read("$.legalshortname.value")); + re.setCountry(asQualifier(j.read("$.country"))); + + break; + case project: + re.setProjectTitle(j.read("$.title.value")); + re.setCode(j.read("$.code.value")); + re.setAcronym(j.read("$.acronym.value")); + re.setContracttype(asQualifier(j.read("$.contracttype"))); + + JSONArray f = j.read("$.fundingtree"); + if (!f.isEmpty()) { + re.setFundingtree(f.stream() + .map(s -> ((LinkedHashMap) s).get("value")) + .collect(Collectors.toList())); + } + + break; + } + return new EntityRelEntity().setSource( + new TypedRow() + .setSourceId(e.getSource().getSourceId()) + .setDeleted(e.getSource().getDeleted()) + .setType(e.getSource().getType()) + .setOaf(serialize(re))); + } + + private static KeyValue asKV(LinkedHashMap j) { + final KeyValue kv = new KeyValue(); + kv.setKey((String) j.get("key")); + kv.setValue((String) j.get("value")); + return kv; + } + + private static void mapTitle(DocumentContext j, RelatedEntity re) { + final JSONArray a = j.read("$.title"); + if (!a.isEmpty()) { + final StructuredProperty sp = asStructuredProperty((LinkedHashMap) a.get(0)); + if (StringUtils.isNotBlank(sp.getValue())) { + re.setTitle(sp); + } + } + } + + private static StructuredProperty asStructuredProperty(LinkedHashMap j) { + final StructuredProperty sp = new StructuredProperty(); + final String value = (String) j.get("value"); + if (StringUtils.isNotBlank(value)) { + sp.setValue((String) j.get("value")); + sp.setQualifier(asQualifier((LinkedHashMap) j.get("qualifier"))); + } + return sp; + } + + public static Qualifier asQualifier(LinkedHashMap j) { + final Qualifier q = new Qualifier(); + + final String classid = j.get("classid"); + if (StringUtils.isNotBlank(classid)) { + q.setClassid(classid); + } + + final String classname = j.get("classname"); + if (StringUtils.isNotBlank(classname)) { + q.setClassname(classname); + } + + final String schemeid = j.get("schemeid"); + if (StringUtils.isNotBlank(schemeid)) { + q.setSchemeid(schemeid); + } + + final String schemename = j.get("schemename"); + if (StringUtils.isNotBlank(schemename)) { + q.setSchemename(schemename); + } + return q; + } + + public static String serialize(final Object o) { + try { + return new ObjectMapper() + .setSerializationInclusion(JsonInclude.Include.NON_NULL) + .writeValueAsString(o); + } catch (JsonProcessingException e) { + throw new IllegalArgumentException("unable to serialize: " + o.toString(), e); + } + } + + public static String removePrefix(final String s) { + if (s.contains("|")) return substringAfter(s, "|"); + return s; + } + + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java new file mode 100644 index 000000000..d87f29452 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java @@ -0,0 +1,24 @@ +package eu.dnetlib.dhp.graph.utils; + +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.cxf.jaxws.JaxWsProxyFactoryBean; + +public class ISLookupClientFactory { + + private static final Log log = LogFactory.getLog(ISLookupClientFactory.class); + + public static ISLookUpService getLookUpService(final String isLookupUrl) { + return getServiceStub(ISLookUpService.class, isLookupUrl); + } + + @SuppressWarnings("unchecked") + private static T getServiceStub(final Class clazz, final String endpoint) { + log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint)); + final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean(); + jaxWsProxyFactory.setServiceClass(clazz); + jaxWsProxyFactory.setAddress(endpoint); + return (T) jaxWsProxyFactory.create(); + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/LicenseComparator.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/LicenseComparator.java new file mode 100644 index 000000000..c4cbfadea --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/LicenseComparator.java @@ -0,0 +1,49 @@ +package eu.dnetlib.dhp.graph.utils; + +import eu.dnetlib.dhp.schema.oaf.Qualifier; + +import java.util.Comparator; + +public class LicenseComparator implements Comparator { + + @Override + public int compare(Qualifier left, Qualifier right) { + + if (left == null && right == null) return 0; + if (left == null) return 1; + if (right == null) return -1; + + String lClass = left.getClassid(); + String rClass = right.getClassid(); + + if (lClass.equals(rClass)) return 0; + + if (lClass.equals("OPEN SOURCE")) return -1; + if (rClass.equals("OPEN SOURCE")) return 1; + + if (lClass.equals("OPEN")) return -1; + if (rClass.equals("OPEN")) return 1; + + if (lClass.equals("6MONTHS")) return -1; + if (rClass.equals("6MONTHS")) return 1; + + if (lClass.equals("12MONTHS")) return -1; + if (rClass.equals("12MONTHS")) return 1; + + if (lClass.equals("EMBARGO")) return -1; + if (rClass.equals("EMBARGO")) return 1; + + if (lClass.equals("RESTRICTED")) return -1; + if (rClass.equals("RESTRICTED")) return 1; + + if (lClass.equals("CLOSED")) return -1; + if (rClass.equals("CLOSED")) return 1; + + if (lClass.equals("UNKNOWN")) return -1; + if (rClass.equals("UNKNOWN")) return 1; + + // Else (but unlikely), lexicographical ordering will do. + return lClass.compareTo(rClass); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/StreamingInputDocumentFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/StreamingInputDocumentFactory.java new file mode 100644 index 000000000..736c9fc28 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/StreamingInputDocumentFactory.java @@ -0,0 +1,253 @@ +package eu.dnetlib.dhp.graph.utils; + +import java.io.StringReader; +import java.io.StringWriter; +import java.util.Arrays; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import javax.xml.stream.*; +import javax.xml.stream.events.Namespace; +import javax.xml.stream.events.StartElement; +import javax.xml.stream.events.XMLEvent; + +import com.google.common.collect.Lists; +import org.apache.solr.common.SolrInputDocument; + +/** + * Optimized version of the document parser, drop in replacement of InputDocumentFactory. + * + *

+ * Faster because: + *

+ *
    + *
  • Doesn't create a DOM for the full document
    • + *
  • Doesn't execute xpaths agains the DOM
    • + *
  • Quickly serialize the 'result' element directly in a string.
    • + *
  • Uses less memory: less pressure on GC and allows more threads to process this in parallel
    • + *
+ * + *

+ * This class is fully reentrant and can be invoked in parallel. + *

+ * + * @author claudio + * + */ +public class StreamingInputDocumentFactory { + + private static final String INDEX_FIELD_PREFIX = "__"; + + private static final String DS_VERSION = INDEX_FIELD_PREFIX + "dsversion"; + + private static final String DS_ID = INDEX_FIELD_PREFIX + "dsid"; + + private static final String RESULT = "result"; + + private static final String INDEX_RESULT = INDEX_FIELD_PREFIX + RESULT; + + private static final String INDEX_RECORD_ID = INDEX_FIELD_PREFIX + "indexrecordidentifier"; + + private static final String outFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'"); + + private final static List dateFormats = Arrays.asList("yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy"); + + private static final String DEFAULTDNETRESULT = "dnetResult"; + + private static final String TARGETFIELDS = "targetFields"; + + private static final String INDEX_RECORD_ID_ELEMENT = "indexRecordIdentifier"; + + private static final String ROOT_ELEMENT = "indexRecord"; + + private static final int MAX_FIELD_LENGTH = 25000; + + private ThreadLocal inputFactory = ThreadLocal.withInitial(() -> XMLInputFactory.newInstance()); + + private ThreadLocal outputFactory = ThreadLocal.withInitial(() -> XMLOutputFactory.newInstance()); + + private ThreadLocal eventFactory = ThreadLocal.withInitial(() -> XMLEventFactory.newInstance()); + + private String version; + + private String dsId; + + private String resultName = DEFAULTDNETRESULT; + + public StreamingInputDocumentFactory(final String version, final String dsId) { + this(version, dsId, DEFAULTDNETRESULT); + } + + public StreamingInputDocumentFactory(final String version, final String dsId, final String resultName) { + this.version = version; + this.dsId = dsId; + this.resultName = resultName; + } + + public SolrInputDocument parseDocument(final String inputDocument) { + + final StringWriter results = new StringWriter(); + final List nsList = Lists.newLinkedList(); + try { + + XMLEventReader parser = inputFactory.get().createXMLEventReader(new StringReader(inputDocument)); + + final SolrInputDocument indexDocument = new SolrInputDocument(new HashMap<>()); + + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + if ((event != null) && event.isStartElement()) { + final String localName = event.asStartElement().getName().getLocalPart(); + + if (ROOT_ELEMENT.equals(localName)) { + nsList.addAll(getNamespaces(event)); + } else if (INDEX_RECORD_ID_ELEMENT.equals(localName)) { + final XMLEvent text = parser.nextEvent(); + String recordId = getText(text); + indexDocument.addField(INDEX_RECORD_ID, recordId); + } else if (TARGETFIELDS.equals(localName)) { + parseTargetFields(indexDocument, parser); + } else if (resultName.equals(localName)) { + copyResult(indexDocument, results, parser, nsList, resultName); + } + } + } + + if (version != null) { + indexDocument.addField(DS_VERSION, version); + } + + if (dsId != null) { + indexDocument.addField(DS_ID, dsId); + } + + if (!indexDocument.containsKey(INDEX_RECORD_ID)) { + indexDocument.clear(); + System.err.println("missing indexrecord id:\n" + inputDocument); + } + + return indexDocument; + } catch (XMLStreamException e) { + return new SolrInputDocument(); + } + } + + private List getNamespaces(final XMLEvent event) { + final List res = Lists.newLinkedList(); + @SuppressWarnings("unchecked") + Iterator nsIter = event.asStartElement().getNamespaces(); + while (nsIter.hasNext()) { + Namespace ns = nsIter.next(); + res.add(ns); + } + return res; + } + + /** + * Parse the targetFields block and add fields to the solr document. + * + * @param indexDocument + * @param parser + * @throws XMLStreamException + */ + protected void parseTargetFields(final SolrInputDocument indexDocument, final XMLEventReader parser) throws XMLStreamException { + + boolean hasFields = false; + + while (parser.hasNext()) { + final XMLEvent targetEvent = parser.nextEvent(); + if (targetEvent.isEndElement() && targetEvent.asEndElement().getName().getLocalPart().equals(TARGETFIELDS)) { + break; + } + + if (targetEvent.isStartElement()) { + final String fieldName = targetEvent.asStartElement().getName().getLocalPart(); + final XMLEvent text = parser.nextEvent(); + + String data = getText(text); + + addField(indexDocument, fieldName, data); + hasFields = true; + } + } + + if (!hasFields) { + indexDocument.clear(); + } + } + + /** + * Copy the /indexRecord/result element and children, preserving namespace declarations etc. + * + * @param indexDocument + * @param results + * @param parser + * @param nsList + * @throws XMLStreamException + */ + protected void copyResult(final SolrInputDocument indexDocument, + final StringWriter results, + final XMLEventReader parser, + final List nsList, + final String dnetResult) throws XMLStreamException { + final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(results); + + for (Namespace ns : nsList) { + eventFactory.get().createNamespace(ns.getPrefix(), ns.getNamespaceURI()); + } + + StartElement newRecord = eventFactory.get().createStartElement("", null, RESULT, null, nsList.iterator()); + + // new root record + writer.add(newRecord); + + // copy the rest as it is + while (parser.hasNext()) { + final XMLEvent resultEvent = parser.nextEvent(); + + // TODO: replace with depth tracking instead of close tag tracking. + if (resultEvent.isEndElement() && resultEvent.asEndElement().getName().getLocalPart().equals(dnetResult)) { + writer.add(eventFactory.get().createEndElement("", null, RESULT)); + break; + } + + writer.add(resultEvent); + } + writer.close(); + indexDocument.addField(INDEX_RESULT, results.toString()); + } + + /** + * Helper used to add a field to a solr doc. It avoids to add empy fields + * + * @param indexDocument + * @param field + * @param value + */ + private final void addField(final SolrInputDocument indexDocument, final String field, final String value) { + String cleaned = value.trim(); + if (!cleaned.isEmpty()) { + // log.info("\n\n adding field " + field.toLowerCase() + " value: " + cleaned + "\n"); + indexDocument.addField(field.toLowerCase(), cleaned); + } + } + + /** + * Helper used to get the string from a text element. + * + * @param text + * @return the + */ + protected final String getText(final XMLEvent text) { + if (text.isEndElement()) // log.warn("skipping because isEndOfElement " + text.asEndElement().getName().getLocalPart()); + return ""; + + final String data = text.asCharacters().getData(); + if (data != null && data.length() > MAX_FIELD_LENGTH) { + return data.substring(0, MAX_FIELD_LENGTH); + } + + return data; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateFactory.java new file mode 100644 index 000000000..27c55fab7 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateFactory.java @@ -0,0 +1,107 @@ +package eu.dnetlib.dhp.graph.utils; + +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import org.apache.commons.lang3.StringUtils; +import org.stringtemplate.v4.ST; + +import java.io.IOException; +import java.util.Collection; +import java.util.List; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.graph.utils.GraphMappingUtils.removePrefix; +import static eu.dnetlib.dhp.graph.utils.XmlSerializationUtils.escapeXml; + +public class TemplateFactory { + + private TemplateResources resources; + + private final static char DELIMITER = '$'; + + public TemplateFactory() { + try { + resources = new TemplateResources(); + } catch (IOException e) { + throw new IllegalStateException(e); + } + } + + public String buildBody(final String type, final List metadata, final List rels, final List children, final List extraInfo) { + ST body = getTemplate(resources.getEntity()); + + body.add("name", type); + body.add("metadata", metadata); + body.add("rels", rels); + body.add("children", children); + body.add("extrainfo", extraInfo); + + return body.render(); + } + + public String getChild(final String name, final String id, final List metadata) { + return getTemplate(resources.getChild()) + .add("name", name) + .add("hasId", !(id == null)) + .add("id", id != null ? escapeXml(removePrefix(id)) : "") + .add("metadata", metadata) + .render(); + } + + public String buildRecord( + final OafEntity entity, + final String schemaLocation, + final String body) { + return getTemplate(resources.getRecord()) + .add("id", escapeXml(removePrefix(entity.getId()))) + .add("dateofcollection", entity.getDateofcollection()) + .add("dateoftransformation", entity.getDateoftransformation()) + .add("schemaLocation", schemaLocation) + .add("it", body) + .render(); + } + + public String getRel(final String type, + final String objIdentifier, + final Collection fields, + final String semanticclass, + final String semantischeme, + final DataInfo info) { + return getTemplate(resources.getRel()) + .add("type", type) + .add("objIdentifier", escapeXml(removePrefix(objIdentifier))) + .add("class", semanticclass) + .add("scheme", semantischeme) + .add("metadata", fields) + .add("inferred", info.getInferred()) + .add("trust", info.getTrust()) + .add("inferenceprovenance", info.getInferenceprovenance()) + .add("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "") + .render(); + } + + public String getInstance(final String resultId, final List instancemetadata, final List webresources) { + return getTemplate(resources.getInstance()) + .add("instanceId", escapeXml(removePrefix(resultId))) + .add("metadata", instancemetadata) + .add("webresources", webresources + .stream() + .filter(StringUtils::isNotBlank) + .map(w -> getWebResource(w)) + .collect(Collectors.toList())) + .render(); + } + + private String getWebResource(final String identifier) { + return getTemplate(resources.getWebresource()) + .add("identifier", escapeXml(identifier)) + .render(); + } + + // HELPERS + + private ST getTemplate(final String res) { + return new ST(res, DELIMITER, DELIMITER); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateResources.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateResources.java new file mode 100644 index 000000000..92aaedfd3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/TemplateResources.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.graph.utils; + +import com.google.common.io.Resources; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; + +public class TemplateResources { + + private String record = read("eu/dnetlib/dhp/graph/template/record.st"); + + private String instance = read("eu/dnetlib/dhp/graph/template/instance.st"); + + private String rel = read("eu/dnetlib/dhp/graph/template/rel.st"); + + private String webresource = read("eu/dnetlib/dhp/graph/template/webresource.st"); + + private String child = read("eu/dnetlib/dhp/graph/template/child.st"); + + private String entity = read("eu/dnetlib/dhp/graph/template/entity.st"); + + private static String read(final String classpathResource) throws IOException { + return Resources.toString(Resources.getResource(classpathResource), StandardCharsets.UTF_8); + } + + public TemplateResources() throws IOException { + + } + + public String getEntity() { + return entity; + } + + public String getRecord() { + return record; + } + + public String getInstance() { + return instance; + } + + public String getRel() { + return rel; + } + + public String getWebresource() { + return webresource; + } + + public String getChild() { + return child; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlRecordFactory.java new file mode 100644 index 000000000..abcf2a7ec --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlRecordFactory.java @@ -0,0 +1,962 @@ +package eu.dnetlib.dhp.graph.utils; + +import com.google.common.base.Joiner; +import com.google.common.base.Splitter; +import com.google.common.collect.Lists; +import com.google.common.collect.Sets; +import com.mycila.xmltool.XMLDoc; +import com.mycila.xmltool.XMLTag; +import eu.dnetlib.dhp.graph.model.JoinedEntity; +import eu.dnetlib.dhp.graph.model.RelatedEntity; +import eu.dnetlib.dhp.graph.model.Tuple2; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.Node; +import org.dom4j.io.OutputFormat; +import org.dom4j.io.SAXReader; +import org.dom4j.io.XMLWriter; + +import javax.xml.transform.*; +import javax.xml.transform.dom.DOMSource; +import javax.xml.transform.stream.StreamResult; +import java.io.IOException; +import java.io.Serializable; +import java.io.StringReader; +import java.io.StringWriter; +import java.util.List; +import java.util.Set; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.graph.utils.GraphMappingUtils.*; +import static eu.dnetlib.dhp.graph.utils.XmlSerializationUtils.*; +import static org.apache.commons.lang3.StringUtils.isNotBlank; +import static org.apache.commons.lang3.StringUtils.substringBefore; + +public class XmlRecordFactory implements Serializable { + + private Set specialDatasourceTypes; + + private ContextMapper contextMapper; + + private String schemaLocation; + + private Set contextes = Sets.newHashSet(); + + private boolean indent = false; + + public XmlRecordFactory( + final ContextMapper contextMapper, final boolean indent, + final String schemaLocation, final Set otherDatasourceTypesUForUI) { + + this.contextMapper = contextMapper; + this.schemaLocation = schemaLocation; + this.specialDatasourceTypes = otherDatasourceTypesUForUI; + + this.indent = indent; + } + + public String build(final JoinedEntity je) { + final OafEntity entity = je.getEntity(); + TemplateFactory templateFactory = new TemplateFactory(); + try { + final List metadata = metadata(je.getType(), entity); + + // rels has to be processed before the contexts because they enrich the contextMap with the funding info. + final List relations = listRelations(je, templateFactory); + + metadata.addAll(buildContexts(getMainType(je.getType()))); + metadata.add(parseDataInfo(entity.getDataInfo())); + + final String body = templateFactory.buildBody( + getMainType(je.getType()), + metadata, + relations, + listChildren(je, templateFactory), listExtraInfo(je)); + + return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); + } catch (final Throwable e) { + throw new RuntimeException(String.format("error building record '%s'", entity.getId()), e); + } + } + + private String printXML(String xml, boolean indent) { + try { + final Document doc = new SAXReader().read(new StringReader(xml)); + OutputFormat format = indent ? OutputFormat.createPrettyPrint() : OutputFormat.createCompactFormat(); + format.setExpandEmptyElements(false); + format.setSuppressDeclaration(true); + StringWriter sw = new StringWriter(); + XMLWriter writer = new XMLWriter(sw, format); + writer.write(doc); + return sw.toString(); + } catch (IOException | DocumentException e) { + throw new IllegalArgumentException("Unable to indent XML. Invalid record:\n" + xml, e); + } + } + + private List metadata(final String type, final OafEntity entity) { + + final List metadata = Lists.newArrayList(); + + if (entity.getCollectedfrom() != null) { + metadata.addAll(entity.getCollectedfrom() + .stream() + .map(kv -> mapKeyValue("collectedfrom", kv)) + .collect(Collectors.toList())); + } + if (entity.getOriginalId() != null) { + metadata.addAll(entity.getOriginalId() + .stream() + .map(s -> asXmlElement("originalId", s)) + .collect(Collectors.toList())); + } + if (entity.getPid() != null) { + metadata.addAll(entity.getPid() + .stream() + .map(p -> mapStructuredProperty("pid", p)) + .collect(Collectors.toList())); + } + + if (GraphMappingUtils.isResult(type)) { + final Result r = (Result) entity; + + if (r.getTitle() != null) { + metadata.addAll(r.getTitle() + .stream() + .map(t -> mapStructuredProperty("title", t)) + .collect(Collectors.toList())); + } + if (r.getBestaccessright() != null) { + metadata.add(mapQualifier("bestaccessright", r.getBestaccessright())); + } + if (r.getAuthor() != null) { + metadata.addAll(r.getAuthor() + .stream() + .map(a -> { + final StringBuilder sb = new StringBuilder(" isNotBlank(sp.getQualifier().getClassid()) && isNotBlank(sp.getValue())) + .forEach(sp -> { + String pidType = escapeXml(sp.getQualifier().getClassid()).replaceAll("\\W", ""); + String pidValue = escapeXml(sp.getValue()); + + // ugly hack: some records provide swapped pidtype and pidvalue + if (authorPidTypes.contains(pidValue.toLowerCase().trim())) { + sb.append(String.format(" %s=\"%s\"", pidValue, pidType)); + } else { + pidType = pidType.replaceAll("\\W", "").replaceAll("\\d", ""); + if (isNotBlank(pidType)) { + sb.append(String.format(" %s=\"%s\"", + pidType, + pidValue.toLowerCase().replaceAll("orcid", ""))); + } + } + }); + } + sb.append(">" + escapeXml(a.getFullname()) + ""); + return sb.toString(); + }).collect(Collectors.toList())); + } + if (r.getContributor() != null) { + metadata.addAll(r.getContributor() + .stream() + .map(c -> asXmlElement("contributor", c.getValue())) + .collect(Collectors.toList())); + } + if (r.getCountry() != null) { + metadata.addAll(r.getCountry() + .stream() + .map(c -> mapQualifier("country", c)) + .collect(Collectors.toList())); + } + if (r.getCoverage() != null) { + metadata.addAll(r.getCoverage() + .stream() + .map(c -> asXmlElement("coverage", c.getValue())) + .collect(Collectors.toList())); + } + if (r.getDateofacceptance() != null) { + metadata.add(asXmlElement("dateofacceptance", r.getDateofacceptance().getValue())); + } + if (r.getDescription() != null) { + metadata.addAll(r.getDescription() + .stream() + .map(c -> asXmlElement("description", c.getValue())) + .collect(Collectors.toList())); + } + if (r.getEmbargoenddate() != null) { + metadata.add(asXmlElement("embargoenddate", r.getEmbargoenddate().getValue())); + } + if (r.getSubject() != null) { + metadata.addAll(r.getSubject() + .stream() + .map(s -> mapStructuredProperty("subject", s)) + .collect(Collectors.toList())); + } + if (r.getLanguage() != null) { + metadata.add(mapQualifier("language", r.getLanguage())); + } + if (r.getRelevantdate() != null) { + metadata.addAll(r.getRelevantdate() + .stream() + .map(s -> mapStructuredProperty("relevantdate", s)) + .collect(Collectors.toList())); + } + if (r.getPublisher() != null) { + metadata.add(asXmlElement("publisher", r.getPublisher().getValue())); + } + if (r.getSource() != null) { + metadata.addAll(r.getSource() + .stream() + .map(c -> asXmlElement("source", c.getValue())) + .collect(Collectors.toList())); + } + if (r.getFormat() != null) { + metadata.addAll(r.getFormat() + .stream() + .map(c -> asXmlElement("format", c.getValue())) + .collect(Collectors.toList())); + } + if (r.getResulttype() != null) { + metadata.add(mapQualifier("resulttype", r.getResulttype())); + } + if (r.getResourcetype() != null) { + metadata.add(mapQualifier("resourcetype", r.getResourcetype())); + } + + metadata.add(mapQualifier("bestaccessright", getBestAccessright(r))); + + if (r.getContext() != null) { + contextes.addAll(r.getContext() + .stream() + .map(c -> c.getId()) + .collect(Collectors.toList())); + if (contextes.contains("dh-ch::subcommunity::2")) { + contextes.add("clarin"); + } + } + } + + switch (EntityType.valueOf(type)) { + case publication: + final Publication pub = (Publication) entity; + + if (pub.getJournal() != null) { + final Journal j = pub.getJournal(); + metadata.add(mapJournal(j)); + } + + break; + case dataset: + final Dataset d = (Dataset) entity; + if (d.getDevice() != null) { + metadata.add(asXmlElement("device", d.getDevice().getValue())); + } + if (d.getLastmetadataupdate() != null) { + metadata.add(asXmlElement("lastmetadataupdate", d.getLastmetadataupdate().getValue())); + } + if (d.getMetadataversionnumber() != null) { + metadata.add(asXmlElement("metadataversionnumber", d.getMetadataversionnumber().getValue())); + } + if (d.getSize() != null) { + metadata.add(asXmlElement("size", d.getSize().getValue())); + } + if (d.getStoragedate() != null) { + metadata.add(asXmlElement("storagedate", d.getStoragedate().getValue())); + } + if (d.getVersion() != null) { + metadata.add(asXmlElement("version", d.getVersion().getValue())); + } + //TODO d.getGeolocation() + + break; + case otherresearchproduct: + final OtherResearchProduct orp = (OtherResearchProduct) entity; + + if (orp.getContactperson() != null) { + metadata.addAll(orp.getContactperson() + .stream() + .map(c -> asXmlElement("contactperson", c.getValue())) + .collect(Collectors.toList())); + } + + if (orp.getContactgroup() != null) { + metadata.addAll(orp.getContactgroup() + .stream() + .map(c -> asXmlElement("contactgroup", c.getValue())) + .collect(Collectors.toList())); + } + if (orp.getTool() != null) { + metadata.addAll(orp.getTool() + .stream() + .map(c -> asXmlElement("tool", c.getValue())) + .collect(Collectors.toList())); + } + break; + case software: + final Software s = (Software) entity; + + if (s.getDocumentationUrl() != null) { + metadata.addAll(s.getDocumentationUrl() + .stream() + .map(c -> asXmlElement("documentationUrl", c.getValue())) + .collect(Collectors.toList())); + } + if (s.getLicense() != null) { + metadata.addAll(s.getLicense() + .stream() + .map(l -> mapStructuredProperty("license", l)) + .collect(Collectors.toList())); + } + if (s.getCodeRepositoryUrl() != null) { + metadata.add(asXmlElement("codeRepositoryUrl", s.getCodeRepositoryUrl().getValue())); + } + if (s.getProgrammingLanguage() != null) { + metadata.add(mapQualifier("programmingLanguage", s.getProgrammingLanguage())); + } + break; + case datasource: + final Datasource ds = (Datasource) entity; + + if (ds.getDatasourcetype() != null) { + mapDatasourceType(metadata, ds.getDatasourcetype()); + } + if (ds.getOpenairecompatibility() != null) { + metadata.add(mapQualifier("openairecompatibility", ds.getOpenairecompatibility())); + } + if (ds.getOfficialname() != null) { + metadata.add(asXmlElement("officialname", ds.getOfficialname().getValue())); + } + if (ds.getEnglishname() != null) { + metadata.add(asXmlElement("englishname", ds.getEnglishname().getValue())); + } + if (ds.getWebsiteurl() != null) { + metadata.add(asXmlElement("websiteurl", ds.getWebsiteurl().getValue())); + } + if (ds.getLogourl() != null) { + metadata.add(asXmlElement("logourl", ds.getLogourl().getValue())); + } + if (ds.getContactemail() != null) { + metadata.add(asXmlElement("contactemail", ds.getContactemail().getValue())); + } + if (ds.getNamespaceprefix() != null) { + metadata.add(asXmlElement("namespaceprefix", ds.getNamespaceprefix().getValue())); + } + if (ds.getLatitude() != null) { + metadata.add(asXmlElement("latitude", ds.getLatitude().getValue())); + } + if (ds.getLongitude() != null) { + metadata.add(asXmlElement("longitude", ds.getLongitude().getValue())); + } + if (ds.getDateofvalidation() != null) { + metadata.add(asXmlElement("dateofvalidation", ds.getDateofvalidation().getValue())); + } + if (ds.getDescription() != null) { + metadata.add(asXmlElement("description", ds.getDescription().getValue())); + } + if (ds.getOdnumberofitems() != null) { + metadata.add(asXmlElement("odnumberofitems", ds.getOdnumberofitems().getValue())); + } + if (ds.getOdnumberofitemsdate() != null) { + metadata.add(asXmlElement("odnumberofitemsdate", ds.getOdnumberofitemsdate().getValue())); + } + if (ds.getOdpolicies() != null) { + metadata.add(asXmlElement("odpolicies", ds.getOdpolicies().getValue())); + } + if (ds.getOdlanguages() != null) { + metadata.addAll(ds.getOdlanguages() + .stream() + .map(c -> asXmlElement("odlanguages", c.getValue())) + .collect(Collectors.toList())); + } + if (ds.getOdcontenttypes() != null) { + metadata.addAll(ds.getOdcontenttypes() + .stream() + .map(c -> asXmlElement("odcontenttypes", c.getValue())) + .collect(Collectors.toList())); + } + if (ds.getAccessinfopackage() != null) { + metadata.addAll(ds.getAccessinfopackage() + .stream() + .map(c -> asXmlElement("accessinfopackage", c.getValue())) + .collect(Collectors.toList())); + } + if (ds.getReleaseenddate() != null) { + metadata.add(asXmlElement("releasestartdate", ds.getReleaseenddate().getValue())); + } + if (ds.getReleaseenddate() != null) { + metadata.add(asXmlElement("releaseenddate", ds.getReleaseenddate().getValue())); + } + if (ds.getMissionstatementurl() != null) { + metadata.add(asXmlElement("missionstatementurl", ds.getMissionstatementurl().getValue())); + } + if (ds.getDataprovider() != null) { + metadata.add(asXmlElement("dataprovider", ds.getDataprovider().getValue().toString())); + } + if (ds.getServiceprovider() != null) { + metadata.add(asXmlElement("serviceprovider", ds.getServiceprovider().getValue().toString())); + } + if (ds.getDatabaseaccesstype() != null) { + metadata.add(asXmlElement("databaseaccesstype", ds.getDatabaseaccesstype().getValue())); + } + if (ds.getDatauploadtype() != null) { + metadata.add(asXmlElement("datauploadtype", ds.getDatauploadtype().getValue())); + } + if (ds.getDatabaseaccessrestriction() != null) { + metadata.add(asXmlElement("databaseaccessrestriction", ds.getDatabaseaccessrestriction().getValue())); + } + if (ds.getDatauploadrestriction() != null) { + metadata.add(asXmlElement("datauploadrestriction", ds.getDatauploadrestriction().getValue())); + } + if (ds.getVersioning() != null) { + metadata.add(asXmlElement("versioning", ds.getVersioning().getValue().toString())); + } + if (ds.getCitationguidelineurl() != null) { + metadata.add(asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); + } + if (ds.getQualitymanagementkind() != null) { + metadata.add(asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue())); + } + if (ds.getPidsystems() != null) { + metadata.add(asXmlElement("pidsystems", ds.getPidsystems().getValue())); + } + if (ds.getCertificates() != null) { + metadata.add(asXmlElement("certificates", ds.getCertificates().getValue())); + } + if (ds.getPolicies() != null) { + metadata.addAll(ds.getPolicies() + .stream() + .map(kv -> mapKeyValue("policies", kv)) + .collect(Collectors.toList())); + } + if (ds.getJournal() != null) { + metadata.add(mapJournal(ds.getJournal())); + } + if (ds.getSubjects() != null) { + metadata.addAll(ds.getSubjects() + .stream() + .map(sp -> mapStructuredProperty("subject", sp)) + .collect(Collectors.toList())); + } + + break; + case organization: + final Organization o = (Organization) entity; + + if (o.getLegalshortname() != null) { + metadata.add(asXmlElement("legalshortname", o.getLegalshortname().getValue())); + } + if (o.getLegalname() != null) { + metadata.add(asXmlElement("legalname", o.getLegalname().getValue())); + } + if (o.getAlternativeNames() != null) { + metadata.addAll(o.getAlternativeNames() + .stream() + .map(c -> asXmlElement("alternativeNames", c.getValue())) + .collect(Collectors.toList())); + } + if (o.getWebsiteurl() != null) { + metadata.add(asXmlElement("websiteurl", o.getWebsiteurl().getValue())); + } + if (o.getLogourl() != null) { + metadata.add(asXmlElement("websiteurl", o.getLogourl().getValue())); + } + + if (o.getEclegalbody() != null) { + metadata.add(asXmlElement("eclegalbody", o.getEclegalbody().getValue())); + } + if (o.getEclegalperson() != null) { + metadata.add(asXmlElement("eclegalperson", o.getEclegalperson().getValue())); + } + if (o.getEcnonprofit() != null) { + metadata.add(asXmlElement("ecnonprofit", o.getEcnonprofit().getValue())); + } + if (o.getEcresearchorganization() != null) { + metadata.add(asXmlElement("ecresearchorganization", o.getEcresearchorganization().getValue())); + } + if (o.getEchighereducation() != null) { + metadata.add(asXmlElement("echighereducation", o.getEchighereducation().getValue())); + } + if (o.getEcinternationalorganization() != null) { + metadata.add(asXmlElement("ecinternationalorganizationeurinterests", o.getEcinternationalorganization().getValue())); + } + if (o.getEcinternationalorganization() != null) { + metadata.add(asXmlElement("ecinternationalorganization", o.getEcinternationalorganization().getValue())); + } + if (o.getEcenterprise() != null) { + metadata.add(asXmlElement("ecenterprise", o.getEcenterprise().getValue())); + } + if (o.getEcsmevalidated() != null) { + metadata.add(asXmlElement("ecsmevalidated", o.getEcsmevalidated().getValue())); + } + if (o.getEcnutscode() != null) { + metadata.add(asXmlElement("ecnutscode", o.getEcnutscode().getValue())); + } + if (o.getCountry() != null) { + metadata.add(mapQualifier("country", o.getCountry())); + } + + break; + case project: + + final Project p = (Project) entity; + + if (p.getWebsiteurl() != null) { + metadata.add(asXmlElement("websiteurl", p.getWebsiteurl().getValue())); + } + if (p.getCode() != null) { + metadata.add(asXmlElement("code", p.getCode().getValue())); + } + if (p.getAcronym() != null) { + metadata.add(asXmlElement("acronym", p.getAcronym().getValue())); + } + if (p.getTitle() != null) { + metadata.add(asXmlElement("title", p.getTitle().getValue())); + } + if (p.getStartdate() != null) { + metadata.add(asXmlElement("startdate", p.getStartdate().getValue())); + } + if (p.getEnddate() != null) { + metadata.add(asXmlElement("enddate", p.getEnddate().getValue())); + } + if (p.getCallidentifier() != null) { + metadata.add(asXmlElement("callidentifier", p.getCallidentifier().getValue())); + } + if (p.getKeywords() != null) { + metadata.add(asXmlElement("keywords", p.getKeywords().getValue())); + } + if (p.getDuration() != null) { + metadata.add(asXmlElement("duration", p.getDuration().getValue())); + } + if (p.getEcarticle29_3() != null) { + metadata.add(asXmlElement("ecarticle29_3", p.getEcarticle29_3().getValue())); + } + if (p.getSubjects() != null) { + metadata.addAll(p.getSubjects() + .stream() + .map(sp -> mapStructuredProperty("subject", sp)) + .collect(Collectors.toList())); + } + if (p.getContracttype() != null) { + metadata.add(mapQualifier("contracttype", p.getContracttype())); + } + if (p.getEcsc39() != null) { + metadata.add(asXmlElement("ecsc39", p.getEcsc39().getValue())); + } + if (p.getContactfullname() != null) { + metadata.add(asXmlElement("contactfullname", p.getContactfullname().getValue())); + } + if (p.getContactfax() != null) { + metadata.add(asXmlElement("contactfax", p.getContactfax().getValue())); + } + if (p.getContactphone() != null) { + metadata.add(asXmlElement("contactphone", p.getContactphone().getValue())); + } + if (p.getContactemail() != null) { + metadata.add(asXmlElement("contactemail", p.getContactemail().getValue())); + } + if (p.getSummary() != null) { + metadata.add(asXmlElement("summary", p.getSummary().getValue())); + } + if (p.getCurrency() != null) { + metadata.add(asXmlElement("currency", p.getCurrency().getValue())); + } + if (p.getTotalcost() != null) { + metadata.add(asXmlElement("totalcost", p.getTotalcost().toString())); + } + if (p.getFundedamount() != null) { + metadata.add(asXmlElement("fundedamount", p.getFundedamount().toString())); + } + if (p.getFundingtree() != null) { + metadata.addAll(p.getFundingtree() + .stream() + .map(ft -> asXmlElement("fundingtree", ft.getValue())) + .collect(Collectors.toList())); + } + + break; + default: + throw new IllegalArgumentException("invalid entity type: " + type); + } + + return metadata; + } + + private void mapDatasourceType(List metadata, final Qualifier dsType) { + metadata.add(mapQualifier("datasourcetype", dsType)); + + if (specialDatasourceTypes.contains(dsType.getClassid())) { + dsType.setClassid("other"); + dsType.setClassname("other"); + } + metadata.add(mapQualifier("datasourcetypeui", dsType)); + } + + private Qualifier getBestAccessright(final Result r) { + Qualifier bestAccessRight = new Qualifier(); + bestAccessRight.setClassid("UNKNOWN"); + bestAccessRight.setClassname("not available"); + bestAccessRight.setSchemeid("dnet:access_modes"); + bestAccessRight.setSchemename("dnet:access_modes"); + + final LicenseComparator lc = new LicenseComparator(); + for (final Instance instance : r.getInstance()) { + if (lc.compare(bestAccessRight, instance.getAccessright()) > 0) { + bestAccessRight = instance.getAccessright(); + } + } + return bestAccessRight; + } + + private List listRelations(final JoinedEntity je, TemplateFactory templateFactory) { + final List rels = Lists.newArrayList(); + + for (final Tuple2 link : je.getLinks()) { + + final Relation rel = link.getRelation(); + final RelatedEntity re = link.getRelatedEntity(); + final String targetType = link.getRelatedEntity().getType(); + + final List metadata = Lists.newArrayList(); + switch (EntityType.valueOf(targetType)) { + case publication: + case dataset: + case otherresearchproduct: + case software: + if (re.getTitle() != null && isNotBlank(re.getTitle().getValue())) { + metadata.add(mapStructuredProperty("title", re.getTitle())); + } + if (isNotBlank(re.getDateofacceptance())) { + metadata.add(asXmlElement("dateofacceptance", re.getDateofacceptance())); + } + if (isNotBlank(re.getPublisher())) { + metadata.add(asXmlElement("publisher", re.getPublisher())); + } + if (isNotBlank(re.getCodeRepositoryUrl())) { + metadata.add(asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl())); + } + if (re.getResulttype() != null & !re.getResulttype().isBlank()) { + metadata.add(mapQualifier("resulttype", re.getResulttype())); + } + if (re.getCollectedfrom() != null) { + metadata.addAll(re.getCollectedfrom() + .stream() + .map(kv -> mapKeyValue("collectedfrom", kv)) + .collect(Collectors.toList())); + } + if (re.getPid() != null) { + metadata.addAll(re.getPid() + .stream() + .map(p -> mapStructuredProperty("pid", p)) + .collect(Collectors.toList())); + } + break; + case datasource: + if (isNotBlank(re.getOfficialname())) { + metadata.add(asXmlElement("officialname", re.getOfficialname())); + } + if (re.getDatasourcetype() != null & !re.getDatasourcetype().isBlank()) { + mapDatasourceType(metadata, re.getDatasourcetype()); + } + if (re.getOpenairecompatibility() != null & !re.getOpenairecompatibility().isBlank()) { + metadata.add(mapQualifier("openairecompatibility", re.getOpenairecompatibility())); + } + break; + case organization: + if (isNotBlank(re.getLegalname())) { + metadata.add(asXmlElement("legalname", re.getLegalname())); + } + if (isNotBlank(re.getLegalshortname())) { + metadata.add(asXmlElement("legalshortname", re.getLegalshortname())); + } + if (re.getCountry() != null & !re.getCountry().isBlank()) { + metadata.add(mapQualifier("country", re.getCountry())); + } + break; + case project: + if (isNotBlank(re.getProjectTitle())) { + metadata.add(asXmlElement("title", re.getProjectTitle())); + } + if (isNotBlank(re.getCode())) { + metadata.add(asXmlElement("code", re.getCode())); + } + if (isNotBlank(re.getAcronym())) { + metadata.add(asXmlElement("acronym", re.getAcronym())); + } + if (re.getContracttype() != null & !re.getContracttype().isBlank()) { + metadata.add(mapQualifier("contracttype", re.getContracttype())); + } + if (re.getFundingtree() != null) { + metadata.addAll(re.getFundingtree() + .stream() + .peek(ft -> fillContextMap(ft)) + .map(ft -> getRelFundingTree(ft)) + .collect(Collectors.toList())); + } + break; + default: + throw new IllegalArgumentException("invalid target type: " + targetType); + + } + final DataInfo info = rel.getDataInfo(); + + rels.add(templateFactory.getRel( + targetType, + rel.getTarget(), + Sets.newHashSet(metadata), + getInverseRelClass(rel.getRelClass()), + getScheme(targetType, re.getType()), + info)); + } + return rels; + } + + private List listChildren(final JoinedEntity je, TemplateFactory templateFactory) { + + final List children = Lists.newArrayList(); + + if (MainEntityType.result.toString().equals(getMainType(je.getType()))) { + final List instances = ((Result) je.getEntity()).getInstance(); + if (instances != null) { + for (final Instance instance : ((Result) je.getEntity()).getInstance()) { + + final List fields = Lists.newArrayList(); + + if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) { + fields.add(mapQualifier("accessright", instance.getAccessright())); + } + if (instance.getCollectedfrom() != null) { + fields.add(mapKeyValue("collectedfrom", instance.getCollectedfrom())); + } + if (instance.getHostedby() != null) { + fields.add(mapKeyValue("hostedby", instance.getHostedby())); + } + if (instance.getDateofacceptance() != null && isNotBlank(instance.getDateofacceptance().getValue())) { + fields.add(asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue())); + } + if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) { + fields.add(mapQualifier("instancetype", instance.getInstancetype())); + } + if (isNotBlank(instance.getDistributionlocation())) { + fields.add(asXmlElement("distributionlocation", instance.getDistributionlocation())); + } + if (instance.getRefereed() != null && isNotBlank(instance.getRefereed().getValue())) { + fields.add(asXmlElement("refereed", instance.getRefereed().getValue())); + } + if (instance.getProcessingchargeamount() != null && isNotBlank(instance.getProcessingchargeamount().getValue())) { + fields.add(asXmlElement("processingchargeamount", instance.getProcessingchargeamount().getValue())); + } + if (instance.getProcessingchargecurrency() != null && isNotBlank(instance.getProcessingchargecurrency().getValue())) { + fields.add(asXmlElement("processingchargecurrency", instance.getProcessingchargecurrency().getValue())); + } + + children.add(templateFactory.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl())); + } + } + final List ext = ((Result) je.getEntity()).getExternalReference(); + if (ext != null) { + for (final ExternalReference er : ((Result) je.getEntity()).getExternalReference()) { + + final List fields = Lists.newArrayList(); + + if (isNotBlank(er.getSitename())) { + fields.add(asXmlElement("sitename", er.getSitename())); + } + if (isNotBlank(er.getLabel())) { + fields.add(asXmlElement("label", er.getLabel())); + } + if (isNotBlank(er.getUrl())) { + fields.add(asXmlElement("url", er.getUrl())); + } + if (isNotBlank(er.getDescription())) { + fields.add(asXmlElement("description", er.getDescription())); + } + if (isNotBlank(er.getUrl())) { + fields.add(mapQualifier("qualifier", er.getQualifier())); + } + if (isNotBlank(er.getRefidentifier())) { + fields.add(asXmlElement("refidentifier", er.getRefidentifier())); + } + if (isNotBlank(er.getQuery())) { + fields.add(asXmlElement("query", er.getQuery())); + } + + children.add(templateFactory.getChild("externalreference", null, fields)); + } + } + } + + return children; + } + + private List listExtraInfo(JoinedEntity je) { + final List extraInfo = je.getEntity().getExtraInfo(); + return extraInfo != null ? extraInfo + .stream() + .map(e -> mapExtraInfo(e)) + .collect(Collectors.toList()) : Lists.newArrayList(); + } + + private List buildContexts(final String type) { + final List res = Lists.newArrayList(); + + if ((contextMapper != null) && !contextMapper.isEmpty() && MainEntityType.result.toString().equals(type)) { + + XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot"); + + for (final String context : contextes) { + + String id = ""; + for (final String token : Splitter.on("::").split(context)) { + id += token; + + final ContextDef def = contextMapper.get(id); + + if (def == null) { + continue; + // throw new IllegalStateException(String.format("cannot find context for id '%s'", id)); + } + + if (def.getName().equals("context")) { + final String xpath = "//context/@id='" + def.getId() + "'"; + if (!document.gotoRoot().rawXpathBoolean(xpath, new Object())) { + document = addContextDef(document.gotoRoot(), def); + } + } + + if (def.getName().equals("category")) { + final String rootId = substringBefore(def.getId(), "::"); + document = addContextDef(document.gotoRoot().gotoTag("//context[./@id='" + rootId + "']", new Object()), def); + } + + if (def.getName().equals("concept")) { + document = addContextDef(document, def).gotoParent(); + } + id += "::"; + } + } + final Transformer transformer = getTransformer(); + for (final org.w3c.dom.Element x : document.gotoRoot().getChildElement()) { + try { + res.add(asStringElement(x, transformer)); + } catch (final TransformerException e) { + throw new RuntimeException(e); + } + } + } + + return res; + } + + private Transformer getTransformer() { + try { + Transformer transformer = TransformerFactory.newInstance().newTransformer(); + transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); + return transformer; + } catch (TransformerConfigurationException e) { + throw new IllegalStateException("unable to create javax.xml.transform.Transformer", e); + } + } + + private XMLTag addContextDef(final XMLTag tag, final ContextDef def) { + tag.addTag(def.getName()).addAttribute("id", def.getId()).addAttribute("label", def.getLabel()); + if ((def.getType() != null) && !def.getType().isEmpty()) { + tag.addAttribute("type", def.getType()); + } + return tag; + } + + private String asStringElement(final org.w3c.dom.Element element, final Transformer transformer) throws TransformerException { + final StringWriter buffer = new StringWriter(); + transformer.transform(new DOMSource(element), new StreamResult(buffer)); + return buffer.toString(); + } + + private void fillContextMap(final String xmlTree) { + + Document fundingPath; + try { + fundingPath = new SAXReader().read(new StringReader(xmlTree)); + } catch (final DocumentException e) { + throw new RuntimeException(e); + } + try { + final Node funder = fundingPath.selectSingleNode("//funder"); + + if (funder != null) { + + final String funderShortName = funder.valueOf("./shortname"); + contextes.add(funderShortName); + + contextMapper.put(funderShortName, new ContextDef(funderShortName, funder.valueOf("./name"), "context", "funding")); + final Node level0 = fundingPath.selectSingleNode("//funding_level_0"); + if (level0 != null) { + final String level0Id = Joiner.on("::").join(funderShortName, level0.valueOf("./name")); + contextMapper.put(level0Id, new ContextDef(level0Id, level0.valueOf("./description"), "category", "")); + final Node level1 = fundingPath.selectSingleNode("//funding_level_1"); + if (level1 == null) { + contextes.add(level0Id); + } else { + final String level1Id = Joiner.on("::").join(level0Id, level1.valueOf("./name")); + contextMapper.put(level1Id, new ContextDef(level1Id, level1.valueOf("./description"), "concept", "")); + final Node level2 = fundingPath.selectSingleNode("//funding_level_2"); + if (level2 == null) { + contextes.add(level1Id); + } else { + final String level2Id = Joiner.on("::").join(level1Id, level2.valueOf("./name")); + contextMapper.put(level2Id, new ContextDef(level2Id, level2.valueOf("./description"), "concept", "")); + contextes.add(level2Id); + } + } + } + } + } catch (final NullPointerException e) { + throw new IllegalArgumentException("malformed funding path: " + xmlTree, e); + } + } + + + + @SuppressWarnings("unchecked") + private String getRelFundingTree(final String xmlTree) { + String funding = ""; + try { + final Document ftree = new SAXReader().read(new StringReader(xmlTree)); + funding = ""; + + funding += getFunderElement(ftree); + + for (final Object o : Lists.reverse(ftree.selectNodes("//fundingtree//*[starts-with(local-name(),'funding_level_')]"))) { + final Element e = (Element) o; + final String _id = e.valueOf("./id"); + funding += "<" + e.getName() + " name=\"" + escapeXml(e.valueOf("./name")) + "\">" + escapeXml(_id) + ""; + } + } catch (final DocumentException e) { + throw new IllegalArgumentException("unable to parse funding tree: " + xmlTree + "\n" + e.getMessage()); + } finally { + funding += ""; + } + return funding; + } + + private String getFunderElement(final Document ftree) { + final String funderId = ftree.valueOf("//fundingtree/funder/id/text()"); + final String funderShortName = ftree.valueOf("//fundingtree/funder/shortname/text()"); + final String funderName = ftree.valueOf("//fundingtree/funder/name/text()"); + final String funderJurisdiction = ftree.valueOf("//fundingtree/funder/jurisdiction/text()"); + + return ""; + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlSerializationUtils.java new file mode 100644 index 000000000..3088828ab --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/XmlSerializationUtils.java @@ -0,0 +1,151 @@ +package eu.dnetlib.dhp.graph.utils; + +import eu.dnetlib.dhp.schema.oaf.*; + +import static eu.dnetlib.dhp.graph.utils.GraphMappingUtils.removePrefix; +import static org.apache.commons.lang3.StringUtils.isBlank; +import static org.apache.commons.lang3.StringUtils.isNotBlank; + +public class XmlSerializationUtils { + + // XML 1.0 + // #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF] + private final static String xml10pattern = "[^" + + "\u0009\r\n" + + "\u0020-\uD7FF" + + "\uE000-\uFFFD" + + "\ud800\udc00-\udbff\udfff" + + "]"; + + public static String mapJournal(Journal j) { + final String attrs = new StringBuilder() + .append(attr("issn", j.getIssnPrinted())) + .append(attr("eissn", j.getIssnOnline())) + .append(attr("lissn", j.getIssnLinking())) + .append(attr("ep", j.getEp())) + .append(attr("iss", j.getIss())) + .append(attr("sp", j.getSp())) + .append(attr("vol", j.getVol())) + .toString() + .trim(); + + return new StringBuilder() + .append("") + .append(escapeXml(j.getName())) + .append("") + .toString(); + } + + private static String attr(final String name, final String value) { + return isNotBlank(value) ? name + "=\"" + escapeXml(value) + "\" " : ""; + } + + public static String mapStructuredProperty(String name, StructuredProperty t) { + return asXmlElement(name, t.getValue(), t.getQualifier(), t.getDataInfo() != null ? t.getDataInfo() : null); + } + + public static String mapQualifier(String name, Qualifier q) { + return asXmlElement(name, "", q, null); + } + + public static String escapeXml(final String value) { + return value + .replaceAll("&", "&") + .replaceAll("<", "<") + .replaceAll(">", ">") + .replaceAll("\"", """) + .replaceAll("'", "'") + .replaceAll(xml10pattern, ""); + } + + public static String parseDataInfo(final DataInfo dataInfo) { + return new StringBuilder() + .append("") + .append(asXmlElement("inferred", dataInfo.getInferred() + "")) + .append(asXmlElement("deletedbyinference", dataInfo.getDeletedbyinference() + "")) + .append(asXmlElement("trust", dataInfo.getTrust() + "")) + .append(asXmlElement("inferenceprovenance", dataInfo.getInferenceprovenance() + "")) + .append(asXmlElement("provenanceaction", null, dataInfo.getProvenanceaction(), null)) + .append("") + .toString(); + } + + private static StringBuilder dataInfoAsAttributes(final StringBuilder sb, final DataInfo info) { + return sb + .append(attr("inferred", info.getInferred() != null ? info.getInferred().toString() : "")) + .append(attr("inferenceprovenance", info.getInferenceprovenance())) + .append(attr("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")) + .append(attr("trust", info.getTrust())); + } + + public static String mapKeyValue(final String name, final KeyValue kv) { + return new StringBuilder() + .append("<") + .append(name) + .append(" name=\"") + .append(escapeXml(kv.getValue())) + .append("\" id=\"") + .append(escapeXml(removePrefix(kv.getKey()))) + .append("\"/>") + .toString(); + } + + public static String mapExtraInfo(final ExtraInfo e) { + return new StringBuilder("") + .append(e.getValue()) + .append("") + .toString(); + } + + public static String asXmlElement(final String name, final String value) { + return asXmlElement(name, value, null, null); + } + + public static String asXmlElement(final String name, final String value, final Qualifier q, final DataInfo info) { + StringBuilder sb = new StringBuilder(); + sb.append("<"); + sb.append(name); + if (q != null) { + sb.append(getAttributes(q)); + } + if (info != null) { + sb + .append(" ") + .append(attr("inferred", info.getInferred() != null ? info.getInferred().toString() : "")) + .append(attr("inferenceprovenance", info.getInferenceprovenance())) + .append(attr("provenanceaction", info.getProvenanceaction() != null ? info.getProvenanceaction().getClassid() : "")) + .append(attr("trust", info.getTrust())); + } + if (isBlank(value)) { + sb.append("/>"); + return sb.toString(); + } + + sb.append(">"); + sb.append(escapeXml(value)); + sb.append(""); + + return sb.toString(); + } + + public static String getAttributes(final Qualifier q) { + if (q == null || q.isBlank()) return ""; + + return new StringBuilder(" ") + .append(attr("classid", q.getClassid())) + .append(attr("classname", q.getClassname())) + .append(attr("schemeid", q.getSchemeid())) + .append(attr("schemename", q.getSchemename())) + .toString(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/META-INF/services/javax.xml.transform.TransformerFactory b/dhp-workflows/dhp-graph-provision/src/main/resources/META-INF/services/javax.xml.transform.TransformerFactory new file mode 100644 index 000000000..b53ca855f --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/META-INF/services/javax.xml.transform.TransformerFactory @@ -0,0 +1 @@ +net.sf.saxon.TransformerFactoryImpl \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_build_adjacency_lists.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_build_adjacency_lists.json new file mode 100644 index 000000000..e63322028 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_build_adjacency_lists.json @@ -0,0 +1,6 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, + {"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequence file to read", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_update_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_update_index.json new file mode 100644 index 000000000..0d45e9e29 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/input_params_update_index.json @@ -0,0 +1,7 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, + {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequence file to read the XML records", "paramRequired": true}, + {"paramName":"f", "paramLongName":"format", "paramDescription": "MDFormat name found in the IS profile", "paramRequired": true}, + {"paramName":"b", "paramLongName":"batchSize", "paramDescription": "size of the batch of documents sent to solr", "paramRequired": false} +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/config-default.xml new file mode 100644 index 000000000..624d3ea76 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hive_db_name + openaire + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18088 + + + spark2EventLogDir + /user/spark/applicationHistory + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/workflow.xml new file mode 100644 index 000000000..350358944 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/workflow.xml @@ -0,0 +1,99 @@ + + + + hive_db_name + the target hive database name + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + + + + ${wf:conf('reuseRecords') eq false} + ${wf:conf('reuseRecords') eq true} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + build_adjacency_lists + eu.dnetlib.dhp.graph.SparkXmlRecordBuilderJob + dhp-graph-provision-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" + --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + -mt yarn + -is ${isLookupUrl} + --sourcePath${sourcePath} + --outputPath${outputPath} + + + + + + + + ${jobTracker} + ${nameNode} + yarn + cluster + to_solr_index + eu.dnetlib.dhp.graph.SparkXmlIndexingJob + dhp-graph-provision-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors=${sparkExecutorCoresForIndexing} + --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" + --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + -mt yarn + -is ${isLookupUrl} + --sourcePath${outputPath}/xml + --format${format} + --batchSize${batchSize} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/child.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/child.st new file mode 100644 index 000000000..89f81e16b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/child.st @@ -0,0 +1,3 @@ +> + $metadata:{ it | $it$ }$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/entity.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/entity.st new file mode 100644 index 000000000..d16f3c3e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/entity.st @@ -0,0 +1,10 @@ + + $metadata:{ it | $it$ }$ + + $rels:{ it | $it$ }$ + + + $children:{ it | $it$ }$ + + +$extrainfo:{ it | $it$ }$ \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/instance.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/instance.st new file mode 100644 index 000000000..64bed05b4 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/instance.st @@ -0,0 +1,4 @@ + + $metadata:{ it | $it$ }$ + $webresources:{ it | $it$ }$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/record.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/record.st new file mode 100644 index 000000000..dea68eab8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/record.st @@ -0,0 +1,17 @@ + + + +
+ $id$ + $dateofcollection$ + $dateoftransformation$ +
+ + + $it$ + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/rel.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/rel.st new file mode 100644 index 000000000..af19ba497 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/rel.st @@ -0,0 +1,4 @@ + + $objIdentifier$ + $metadata:{ it | $it$ }$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/webresource.st b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/webresource.st new file mode 100644 index 000000000..7ff6c5d7f --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/graph/template/webresource.st @@ -0,0 +1,3 @@ + + $identifier$ + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java new file mode 100644 index 000000000..a9d696bea --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java @@ -0,0 +1,66 @@ +package eu.dnetlib.dhp.graph; + +import eu.dnetlib.dhp.graph.model.EntityRelEntity; +import eu.dnetlib.dhp.graph.model.RelatedEntity; +import eu.dnetlib.dhp.graph.utils.GraphMappingUtils; +import org.codehaus.jackson.map.ObjectMapper; +import org.junit.Before; +import org.junit.Test; + +import java.io.IOException; +import java.io.InputStreamReader; + +public class MappingUtilsTest { + + private GraphMappingUtils utils; + + @Before + public void setUp() { + utils = new GraphMappingUtils(); + } + + @Test + public void testOafMappingDatasource() throws IOException { + + final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("datasource.json")); + final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); + e.getSource().setType("datasource"); + + final EntityRelEntity out = utils.asRelatedEntity(e); + System.out.println(out); + + } + + //@Test + public void testOafMappingResult() throws IOException { + + final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("result.json")); + final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); + + final EntityRelEntity out = utils.asRelatedEntity(e); + System.out.println(out); + + } + + @Test + public void testOafMappingSoftware() throws IOException { + + final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("software.json")); + final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); + + final EntityRelEntity out = utils.asRelatedEntity(e); + System.out.println(out); + + } + + + @Test + public void testParseRelatedEntity() throws IOException { + + final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json")); + final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class); + + System.out.println(e); + + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java new file mode 100644 index 000000000..2a3c343ec --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java @@ -0,0 +1,55 @@ +package eu.dnetlib.dhp.graph; + +import eu.dnetlib.dhp.graph.utils.ContextMapper; +import org.apache.commons.io.FileUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.spark.sql.SparkSession; +import org.junit.After; +import org.junit.Before; +import org.junit.Test; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class XmlRecordFactoryTest { + + private static final Log log = LogFactory.getLog(XmlRecordFactoryTest.class); + + private Path testDir; + + @Before + public void setup() throws IOException { + testDir = Files.createTempDirectory(getClass().getSimpleName()); + log.info("created test directory " + testDir.toString()); + } + + @After + public void tearDown() throws IOException { + FileUtils.deleteDirectory(testDir.toFile()); + log.info("deleted test directory " + testDir.toString()); + } + + @Test + public void testXmlSerialization() throws Exception { + + final SparkSession spark = SparkSession + .builder() + .appName(SparkXmlRecordBuilderJob.class.getSimpleName()) + .master("local[*]") + .getOrCreate(); + + final String inputDir = testDir.toString() + "/3_joined_entities"; + FileUtils.forceMkdir(new File(inputDir)); + FileUtils.copyFile(new File("/Users/claudio/Downloads/joined_entities-part-00000"), new File(inputDir + "/joined_entities-part-00000")); + + final ContextMapper ctx = ContextMapper.fromIS("https://dev-openaire.d4science.org:443/is/services/isLookUp"); + + final GraphJoiner g = new GraphJoiner(spark, ctx, inputDir, testDir.toString()); + + g.asXML(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json new file mode 100644 index 000000000..c26154c1e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json @@ -0,0 +1 @@ +{"source":{"sourceId":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","targetId":null,"deleted":false,"oaf":"{\"datasourcetype\":{\"classid\":\"crissystem\",\"classname\":\"CRIS 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\ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json new file mode 100644 index 000000000..25c92baa3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json @@ -0,0 +1,5 @@ +{ + "id": "20|nih_________::6b8108b6d6399f7163a6a7ccdd0efc2d", + "type": "organization", + "legalname": "MCGILL UNIVERSITY" +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json new file mode 100644 index 000000000..5d6c3f29b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json @@ -0,0 +1 @@ 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1.0.5-SNAPSHOT + 1.1.6-SNAPSHOT ../ @@ -18,6 +18,7 @@ dhp-distcp dhp-graph-mapper dhp-dedup + dhp-graph-provision dhp-actionmanager diff --git a/pom.xml b/pom.xml index aedf5ebff..7f5e1e3dc 100644 --- a/pom.xml +++ b/pom.xml @@ -1,215 +1,282 @@ - + - 4.0.0 - eu.dnetlib.dhp - dhp - 1.0.5-SNAPSHOT - pom + 4.0.0 + eu.dnetlib.dhp + dhp + 1.1.6-SNAPSHOT + pom - http://www.d-net.research-infrastructures.eu + http://www.d-net.research-infrastructures.eu - - - The Apache Software License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.txt - repo - A business-friendly OSS license - - + + + The Apache Software License, Version 2.0 + http://www.apache.org/licenses/LICENSE-2.0.txt + repo + A business-friendly OSS license + + - - dhp-build - dhp-schemas - dhp-common - dhp-workflows - + + dhp-build + dhp-schemas + dhp-common + dhp-workflows + - - Redmine - https://issue.openaire.research-infrastructures.eu/projects/openaire - + + Redmine + https://issue.openaire.research-infrastructures.eu/projects/openaire + - - jenkins - https://jenkins-dnet.d4science.org/ - + + jenkins + https://jenkins-dnet.d4science.org/ + - - scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git - scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git - https://code-repo.d4science.org/D-Net/dnet-hadoop/ - HEAD - + + scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git + scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git + https://code-repo.d4science.org/D-Net/dnet-hadoop/ + HEAD + - - + + - - - dnet45-releases - D-Net 45 releases - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases - default - - false - - - true - - - - cloudera - Cloudera Repository - https://repository.cloudera.com/artifactory/cloudera-repos - - true - - - false - - - + + + dnet45-releases + D-Net 45 releases + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases + default + + false + + + true + + + + cloudera + Cloudera Repository + https://repository.cloudera.com/artifactory/cloudera-repos + + true + + + false + + + - - - junit - junit - 4.12 - test - + + + junit + junit + 4.12 + test + - - org.mockito - mockito-core - 2.7.22 - test - + + org.mockito + mockito-core + 2.7.22 + test + - + - - - - org.apache.hadoop - hadoop-hdfs + + + + org.apache.hadoop + hadoop-hdfs + ${dhp.hadoop.version} + provided + + + org.apache.hadoop + hadoop-common ${dhp.hadoop.version} provided org.apache.hadoop hadoop-client - ${dhp.hadoop.version} - provided - - - org.apache.spark - spark-core_2.11 - ${dhp.spark.version} - provided - - - org.apache.spark - spark-sql_2.11 - ${dhp.spark.version} - provided - - - org.apache.spark - spark-graphx_2.11 - ${dhp.spark.version} - provided - + ${dhp.hadoop.version} + provided + + + org.apache.spark + spark-core_2.11 + ${dhp.spark.version} + provided + + + org.apache.spark + spark-sql_2.11 + ${dhp.spark.version} + provided + + + org.apache.spark + spark-graphx_2.11 + ${dhp.spark.version} + provided + - - org.apache.commons - commons-lang3 - ${dhp.commons.lang.version} - + + org.apache.commons + commons-lang3 + ${dhp.commons.lang.version} + - - commons-codec - commons-codec - 1.9 - + + commons-codec + commons-codec + 1.9 + - - commons-io - commons-io - 2.4 - + + commons-io + commons-io + 2.4 + - - commons-cli - commons-cli - 1.2 - provided - + + commons-cli + commons-cli + 1.2 + provided + net.sf.saxon Saxon-HE - 9.5.1-5 + 9.9.1-6 + + + + dom4j + dom4j + 1.6.1 + + + + xml-apis + xml-apis + 1.4.01 + + + + jaxen + jaxen + 1.1.6 + + + + com.mycila.xmltool + xmltool + 3.3 - dom4j - dom4j - 1.6.1 + org.apache.solr + solr-solrj + 7.5.0 + + + * + * + + + + + com.lucidworks.spark + spark-solr + 3.6.0 + + + * + * + + - xml-apis - xml-apis - 1.4.01 + org.apache.httpcomponents + httpclient + 4.5.3 + + + org.apache.httpcomponents + httpmime + 4.5.3 + + + org.noggit + noggit + 0.8 + + + org.apache.zookeeper + zookeeper + 3.4.11 - jaxen - jaxen - 1.1.6 - + net.schmizz + sshj + 0.10.0 + test + - - net.schmizz - sshj - 0.10.0 - test - + + com.fasterxml.jackson.core + jackson-core + ${dhp.jackson.version} + provided + - - com.fasterxml.jackson.core - jackson-core - ${dhp.jackson.version} - provided - - - - com.fasterxml.jackson.core - jackson-annotations - ${dhp.jackson.version} - provided - - - com.fasterxml.jackson.core - jackson-databind - ${dhp.jackson.version} - provided - + + com.fasterxml.jackson.core + jackson-annotations + ${dhp.jackson.version} + provided + + + com.fasterxml.jackson.core + jackson-databind + ${dhp.jackson.version} + provided + + + eu.dnetlib + dnet-pace-core + 4.0.0 + eu.dnetlib - dnet-pace-core - 4.0.0-SNAPSHOT + cnr-rmi-api + [2.0.0,3.0.0) - - javax.persistence - javax.persistence-api - 2.2 - provided + org.apache.cxf + cxf-rt-transports-http + 3.1.5 + + javax.persistence + javax.persistence-api + 2.2 + provided + com.rabbitmq @@ -231,196 +298,183 @@ secondstring 1.0.0 - - org.apache.oozie - oozie-client - ${dhp.oozie.version} - provided - - - - slf4j-simple - org.slf4j - - + org.mongodb + mongo-java-driver + ${mongodb.driver.version} + + + org.antlr + stringtemplate + 4.0 - - - - target - target/classes - ${project.artifactId}-${project.version} - target/test-classes - - - - org.apache.maven.plugins - maven-compiler-plugin - ${maven.compiler.plugin.version} - - 1.8 - 1.8 - ${project.build.sourceEncoding} - - + + org.apache.oozie + oozie-client + ${dhp.oozie.version} + provided + + + + slf4j-simple + org.slf4j + + + + + - - org.apache.maven.plugins - maven-jar-plugin - 3.0.2 - + + target + target/classes + ${project.artifactId}-${project.version} + target/test-classes + + + + org.apache.maven.plugins + maven-compiler-plugin + ${maven.compiler.plugin.version} + + 1.8 + 1.8 + ${project.build.sourceEncoding} + + - - org.apache.maven.plugins - maven-source-plugin - 3.0.1 - - - attach-sources - verify - - jar-no-fork - - - - + + org.apache.maven.plugins + maven-jar-plugin + 3.0.2 + - - org.apache.maven.plugins - maven-surefire-plugin - 2.19.1 - - true - - - - org.apache.maven.plugins - maven-javadoc-plugin - 2.10.4 - - true - - - - org.apache.maven.plugins - maven-dependency-plugin - 3.0.0 - + + org.apache.maven.plugins + maven-source-plugin + 3.0.1 + + + attach-sources + verify + + jar-no-fork + + + + - - org.codehaus.mojo - build-helper-maven-plugin - 1.12 - - - - - - org.apache.maven.plugins - maven-release-plugin - 2.5.3 - - - org.jacoco - jacoco-maven-plugin - 0.7.9 - - - **/schemas/* - **/com/cloudera/**/* - **/org/apache/avro/io/**/* - - - - - default-prepare-agent - - prepare-agent - - - - default-report - prepare-package - - report - - - - - - net.alchim31.maven - scala-maven-plugin - 4.0.1 - - - scala-compile-first - initialize - - add-source - compile - - - - scala-test-compile - process-test-resources - - testCompile - - - - - ${scala.version} - - - + + org.apache.maven.plugins + maven-surefire-plugin + 2.19.1 + + true + + + + org.apache.maven.plugins + maven-javadoc-plugin + 2.10.4 + + true + + + + org.apache.maven.plugins + maven-dependency-plugin + 3.0.0 + - - - org.apache.maven.wagon - wagon-ssh - 2.10 - - - - - - dnet45-snapshots - DNet45 Snapshots - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots - default - - - dnet45-releases - http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases - - - - - - org.apache.maven.plugins - maven-javadoc-plugin - 2.10.4 - - true - - - - + + org.codehaus.mojo + build-helper-maven-plugin + 1.12 + + + + + + org.apache.maven.plugins + maven-release-plugin + 2.5.3 + + + org.jacoco + jacoco-maven-plugin + 0.7.9 + + + **/schemas/* + **/com/cloudera/**/* + **/org/apache/avro/io/**/* + + + + + default-prepare-agent + + prepare-agent + + + + default-report + prepare-package + + report + + + + - - UTF-8 - UTF-8 - 3.6.0 - 2.22.2 - cdh5.9.2 - 2.6.0-${dhp.cdh.version} - 4.1.0-${dhp.cdh.version} - 2.4.0.cloudera2 - 2.9.6 - 3.5 - 2.11.12 - + + + + + org.apache.maven.wagon + wagon-ssh + 2.10 + + + + + + dnet45-snapshots + DNet45 Snapshots + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots + default + + + dnet45-releases + http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases + + + + + + org.apache.maven.plugins + maven-javadoc-plugin + 2.10.4 + + true + + + + + + + UTF-8 + UTF-8 + 3.6.0 + 2.22.2 + cdh5.9.2 + 2.6.0-${dhp.cdh.version} + 4.1.0-${dhp.cdh.version} + 2.4.0.cloudera2 + 2.9.6 + 3.5 + 2.11.12 + 3.4.2 +